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View Code? Open in Web Editor NEWCopy number caller for long read data including SNV utilization
License: MIT License
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Error due to undesirable use of an alternative contig of the reference genome
Hello,
I encountered an error related to the presence of an alternative contig on which Spectre wanted to make the CNV call, whereas I only wanted to make the call on the canonical contigs.
Even though I had specified the contigs I wanted, with the --only-chr argument and the *.regions.bed.gz files were generated specifically on the canonical contigs, Spectre persists in wanting to make the call on the contig HSCHR16_RANDOM_CTG1 present in the reference genome that I am using.
singularity exec --bind /srv:/srv spectre.0.2.0.sif spectre CNVCaller \
--coverage mosdepth/Sample1.regions.bed.gz \
--sample-id Sample1 \
--output-dir results \
--blacklist grch38_blacklist_spectre.bed \
--only-chr chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY \
-0 \
--reference /srv/nfs/ngs-stockage/NGS_Bioinfo/Nanopore/HCL_SNP_ONT/REF/GRCh38.p13.primary_assembly.decoy.fa
[email protected]@ge156378-vm1:~/testardqu/tickets/28452/Spectre$ singularity exec --bind /srv:/srv spectre.0.2.0.sif spectre CNVCaller \
> --coverage mosdepth/Sample1.regions.bed.gz \
> --sample-id Sample1 \
> --output-dir results \
> --blacklist grch38_blacklist_spectre.bed \
> --only-chr chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY \
> -0 \
> --reference /srv/nfs/ngs-stockage/NGS_Bioinfo/Nanopore/HCL_SNP_ONT/REF/GRCh38.p13.primary_assembly.decoy.fa
spectre::2024-04-04 17:30:22,922::INFO::spectre.spectre> Spectre input: CNVCaller --coverage mosdepth/Sample1.regions.bed.gz --sample-id Sample1 --output-dir results --blacklist grch38_blacklist_spectre.bed --only-chr chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY -0 --reference /srv/nfs/ngs-stockage/NGS_Bioinfo/Nanopore/HCL_SNP_ONT/REF/GRCh38.p13.primary_assembly.decoy.fa
spectre::2024-04-04 17:30:22,922::DEBUG::spectre.spectre> Debug output is enabled
spectre::2024-04-04 17:30:22,922::INFO::spectre.spectre> Spectre version: 0.2.0
spectre::2024-04-04 17:30:22,922::INFO::spectre.spectre> Starting spectre
spectre::2024-04-04 17:30:22,922::INFO::spectre.spectre> Evaluate if a new .mdr file needs to be created
spectre::2024-04-04 17:30:22,923::INFO::spectre.spectre> Looking for default metadata.mdr in output directory
spectre::2024-04-04 17:30:22,923::INFO::spectre.spectre> Using existing metadata file
spectre::2024-04-04 17:30:22,929::DEBUG::spectre.spectre> genome: ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY', 'HSCHR16_RANDOM_CTG1']
spectre::2024-04-04 17:30:22,929::INFO::spectre.spectreCNV> Spectre calculating for: mosdepth/Sample1.regions.bed.gz
spectre::2024-04-04 17:30:22,929::INFO::spectre.spectreCNV> Data normalization and outlier removal (right tail)
spectre::2024-04-04 17:30:22,930::DEBUG::spectre.analysis.analysis> coverage file: mosdepth/Sample1.regions.bed.gz
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
spectre::2024-04-04 17:30:23,191::INFO::spectre.analysis.analysis> Determined bin size from Mosdepth coverage: 1000
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
[W::tbx_parse1] Coordinate <= 0 detected. Did you forget to use the -0 option?
Traceback (most recent call last):
File "/usr/local/bin/spectre", line 8, in <module>
sys.exit(main())
^^^^^^
File "/usr/local/lib/python3.11/site-packages/spectre/spectre.py", line 614, in main
spectre_run.spectre_exe()
File "/usr/local/lib/python3.11/site-packages/spectre/spectre.py", line 349, in spectre_exe
spectre_main.cnv_call()
File "/usr/local/lib/python3.11/site-packages/spectre/spectreCNV.py", line 87, in cnv_call
self.cnv_analysis.data_normalization()
File "/usr/local/lib/python3.11/site-packages/spectre/analysis/analysis.py", line 102, in data_normalization
for tbx_line in coverage_file_tabix.fetch(reference_chromosome):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "pysam/libctabix.pyx", line 507, in pysam.libctabix.TabixFile.fetch
ValueError: could not create iterator for region 'HSCHR16_RANDOM_CTG1'I solved the problem by using the new reference genome produced by the following command :
samtools faidx /srv/nfs/ngs-stockage/NGS_Bioinfo/Nanopore/HCL_SNP_ONT/REF/GRCh38.p13.primary_assembly.decoy.fa chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY | bgzip -c > GRCh38.p13.canonical.fa.gz
samtools faidx GRCh38.p13.canonical.fa.gzI don't know if it's a bug or my fault, but I couldn't find any instructions on how to handle alternative contigs in the Spectre README.
Regards.
CNV caller min_cnv_len
When spectre.py CNVcaller --help is used the minimum CNV length option is listed as "min_cnv_len" but should be changed to "min-cnv-len".
Error with --population parameter
Hello,
I've tried running a Spectrum analysis with the --population parameter, to get CNV calls for all patients, but it doesn't work.
singularity exec --bind /srv:/srv spectre.0.2.0.sif spectre CNVCaller \
--coverage mosdepth/Sample1_regions.bed.gz mosdepth/Sample2_regions.bed.gz mosdepth/Sample3_regions.bed.gz mosdepth/Sample4_regions.bed.gz mosdepth/Sample5_regions.bed.gz mosdepth/Sample6_regions.bed.gz mosdepth/Sample7_regions.bed.gz mosdepth/Sample8_regions.bed.gz mosdepth/Sample9_regions.bed.gz mosdepth/Sample10_regions.bed.gz mosdepth/Sample11_regions.bed.gz mosdepth/Sample12_regions.bed.gz mosdepth/Sample13_regions.bed.gz mosdepth/Sample14_regions.bed.gz mosdepth/Sample15_regions.bed.gz mosdepth/Sample16_regions.bed.gz mosdepth/Sample17_regions.bed.gz mosdepth/Sample18_regions.bed.gz mosdepth/Sample19_regions.bed.gz mosdepth/Sample20_regions.bed.gz mosdepth/Sample21_regions.bed.gz mosdepth/Sample22_regions.bed.gz mosdepth/Sample23_regions.bed.gz mosdepth/Sample24_regions.bed.gz mosdepth/Sample25_regions.bed.gz mosdepth/Sample26_regions.bed.gz \
--sample-id Sample1 Sample2 Sample3 Sample4 Sample5 Sample6 Sample7 Sample8 Sample9 Sample10 Sample11 Sample12 Sample13 Sample14 Sample15 Sample16 Sample17 Sample18 Sample19 Sample20 Sample21 Sample22 Sample23 Sample24 Sample25 Sample26 \
--output-dir results_test \
--blacklist grch38_blacklist_spectre.bed \
--only-chr chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY \
-0 \
--population \
--reference GRCh38.p13.canonical.fa.gz
spectre::2024-04-08 10:11:40,663::INFO::spectre.spectre> Spectre input: CNVCaller --coverage mosdepth/Sample1_regions.bed.gz mosdepth/Sample2_regions.bed.gz mosdepth/Sample3_regions.bed.gz mosdepth/Sample4_regions.bed.gz mosdepth/Sample5_regions.bed.gz mosdepth/Sample6_regions.bed.gz mosdepth/Sample7_regions.bed.gz mosdepth/Sample8_regions.bed.gz mosdepth/Sample9_regions.bed.gz mosdepth/Sample10_regions.bed.gz mosdepth/Sample11_regions.bed.gz mosdepth/Sample12_regions.bed.gz mosdepth/Sample13_regions.bed.gz mosdepth/Sample14_regions.bed.gz mosdepth/Sample15_regions.bed.gz mosdepth/Sample16_regions.bed.gz mosdepth/Sample17_regions.bed.gz mosdepth/Sample18_regions.bed.gz mosdepth/Sample19_regions.bed.gz mosdepth/Sample20_regions.bed.gz mosdepth/Sample21_regions.bed.gz mosdepth/Sample22_regions.bed.gz mosdepth/Sample23_regions.bed.gz mosdepth/Sample24_regions.bed.gz mosdepth/Sample25_regions.bed.gz mosdepth/Sample26_regions.bed.gz --sample-id Sample1 Sample2 Sample3 Sample4 Sample5 Sample6 Sample7 Sample8 Sample9 Sample10 Sample11 Sample12 Sample13 Sample14 Sample15 Sample16 Sample17 Sample18 Sample19 Sample20 Sample21 Sample22 Sample23 Sample24 Sample25 Sample26 --output-dir results_test --blacklist grch38_blacklist_spectre.bed --only-chr chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY -0 --population --reference GRCh38.p13.canonical.fa.gz
spectre::2024-04-08 10:11:40,663::DEBUG::spectre.spectre> Debug output is enabled
spectre::2024-04-08 10:11:40,663::INFO::spectre.spectre> Spectre version: 0.2.0
spectre::2024-04-08 10:11:40,663::INFO::spectre.spectre> Starting spectre
spectre::2024-04-08 10:11:40,663::INFO::spectre.spectre> Evaluate if a new .mdr file needs to be created
spectre::2024-04-08 10:11:40,663::INFO::spectre.spectre> Looking for default metadata.mdr in output directory
spectre::2024-04-08 10:11:40,663::INFO::spectre.spectre> No metadata file found in
spectre::2024-04-08 10:11:40,664::INFO::spectre.spectre> Extracting metadata from /srv/scratch/testardqu/tickets/28452/Spectre/GRCh38.p13.canonical.fa.gz
spectre::2024-04-08 10:11:40,664::INFO::spectre.util.metadata.metadataCollector> Reading >chr1
spectre::2024-04-08 10:11:40,665::INFO::spectre.util.metadata.metadataCollector> Found No 1 N region: chr1:1-9999
spectre::2024-04-08 10:11:40,699::INFO::spectre.util.metadata.metadataCollector> Found No 2 N region: chr1:207666-257665
spectre::2024-04-08 10:11:40,709::INFO::spectre.util.metadata.metadataCollector> Found No 3 N region: chr1:297968-347967
spectre::2024-04-08 10:11:40,742::INFO::spectre.util.metadata.metadataCollector> Found No 4 N region: chr1:535988-585987
spectre::2024-04-08 10:11:41,064::INFO::spectre.util.metadata.metadataCollector> Found No 5 N region: chr1:2702781-2746289
spectre::2024-04-08 10:11:42,596::INFO::spectre.util.metadata.metadataCollector> Found No 6 N region: chr1:12954384-13004383
spectre::2024-04-08 10:11:43,172::INFO::spectre.util.metadata.metadataCollector> Found No 7 N region: chr1:16799163-16849162
spectre::2024-04-08 10:11:45,075::INFO::spectre.util.metadata.metadataCollector> Found No 8 N region: chr1:29552233-29553834
spectre::2024-04-08 10:11:59,234::INFO::spectre.util.metadata.metadataCollector> Found No 9 N region: chr1:121757932-121757936
spectre::2024-04-08 10:11:59,234::INFO::spectre.util.metadata.metadataCollector> Found No 10 N region: chr1:121757973-121758072
spectre::2024-04-08 10:11:59,236::INFO::spectre.util.metadata.metadataCollector> Found No 11 N region: chr1:121768152-121768251
spectre::2024-04-08 10:11:59,237::INFO::spectre.util.metadata.metadataCollector> Found No 12 N region: chr1:121776357-121776456
spectre::2024-04-08 10:11:59,238::INFO::spectre.util.metadata.metadataCollector> Found No 13 N region: chr1:121778965-121779064
spectre::2024-04-08 10:11:59,238::INFO::spectre.util.metadata.metadataCollector> Found No 14 N region: chr1:121781090-121781189
spectre::2024-04-08 10:11:59,240::INFO::spectre.util.metadata.metadataCollector> Found No 15 N region: chr1:121792611-121792710
spectre::2024-04-08 10:11:59,240::INFO::spectre.util.metadata.metadataCollector> Found No 16 N region: chr1:121796598-121796697
spectre::2024-04-08 10:11:59,241::INFO::spectre.util.metadata.metadataCollector> Found No 17 N region: chr1:121799683-121799782
spectre::2024-04-08 10:11:59,242::INFO::spectre.util.metadata.metadataCollector> Found No 18 N region: chr1:121804894-121804993
spectre::2024-04-08 10:11:59,242::INFO::spectre.util.metadata.metadataCollector> Found No 19 N region: chr1:121807490-121807589
spectre::2024-04-08 10:11:59,243::INFO::spectre.util.metadata.metadataCollector> Found No 20 N region: chr1:121810201-121810300
spectre::2024-04-08 10:11:59,243::INFO::spectre.util.metadata.metadataCollector> Found No 21 N region: chr1:121813372-121813471
spectre::2024-04-08 10:11:59,244::INFO::spectre.util.metadata.metadataCollector> Found No 22 N region: chr1:121815631-121815730
spectre::2024-04-08 10:11:59,245::INFO::spectre.util.metadata.metadataCollector> Found No 23 N region: chr1:121823518-121823617
spectre::2024-04-08 10:11:59,246::INFO::spectre.util.metadata.metadataCollector> Found No 24 N region: chr1:121826494-121826593
spectre::2024-04-08 10:11:59,246::INFO::spectre.util.metadata.metadataCollector> Found No 25 N region: chr1:121829415-121829514
spectre::2024-04-08 10:11:59,249::INFO::spectre.util.metadata.metadataCollector> Found No 26 N region: chr1:121845841-121845940
spectre::2024-04-08 10:11:59,250::INFO::spectre.util.metadata.metadataCollector> Found No 27 N region: chr1:121851570-121851669
spectre::2024-04-08 10:11:59,250::INFO::spectre.util.metadata.metadataCollector> Found No 28 N region: chr1:121856465-121856564
spectre::2024-04-08 10:11:59,252::INFO::spectre.util.metadata.metadataCollector> Found No 29 N region: chr1:121867000-121867099
spectre::2024-04-08 10:11:59,253::INFO::spectre.util.metadata.metadataCollector> Found No 30 N region: chr1:121870003-121870102
spectre::2024-04-08 10:11:59,253::INFO::spectre.util.metadata.metadataCollector> Found No 31 N region: chr1:121873290-121873389
spectre::2024-04-08 10:11:59,256::INFO::spectre.util.metadata.metadataCollector> Found No 32 N region: chr1:121890873-121890972
spectre::2024-04-08 10:11:59,256::INFO::spectre.util.metadata.metadataCollector> Found No 33 N region: chr1:121893132-121893231
spectre::2024-04-08 10:11:59,257::INFO::spectre.util.metadata.metadataCollector> Found No 34 N region: chr1:121898418-121898517
spectre::2024-04-08 10:11:59,258::INFO::spectre.util.metadata.metadataCollector> Found No 35 N region: chr1:121902342-121902441
spectre::2024-04-08 10:11:59,259::INFO::spectre.util.metadata.metadataCollector> Found No 36 N region: chr1:121911119-121911218
spectre::2024-04-08 10:11:59,260::INFO::spectre.util.metadata.metadataCollector> Found No 37 N region: chr1:121914062-121914161
spectre::2024-04-08 10:11:59,260::INFO::spectre.util.metadata.metadataCollector> Found No 38 N region: chr1:121916621-121916720
spectre::2024-04-08 10:11:59,261::INFO::spectre.util.metadata.metadataCollector> Found No 39 N region: chr1:121923482-121923581
spectre::2024-04-08 10:11:59,262::INFO::spectre.util.metadata.metadataCollector> Found No 40 N region: chr1:121926655-121926754
spectre::2024-04-08 10:11:59,263::INFO::spectre.util.metadata.metadataCollector> Found No 41 N region: chr1:121930672-121930771
spectre::2024-04-08 10:11:59,263::INFO::spectre.util.metadata.metadataCollector> Found No 42 N region: chr1:121935105-121935204
spectre::2024-04-08 10:11:59,264::INFO::spectre.util.metadata.metadataCollector> Found No 43 N region: chr1:121940535-121940634
spectre::2024-04-08 10:11:59,265::INFO::spectre.util.metadata.metadataCollector> Found No 44 N region: chr1:121944280-121944379
spectre::2024-04-08 10:11:59,265::INFO::spectre.util.metadata.metadataCollector> Found No 45 N region: chr1:121946982-121947081
spectre::2024-04-08 10:11:59,266::INFO::spectre.util.metadata.metadataCollector> Found No 46 N region: chr1:121950294-121950393
spectre::2024-04-08 10:11:59,266::INFO::spectre.util.metadata.metadataCollector> Found No 47 N region: chr1:121953308-121953407
spectre::2024-04-08 10:11:59,267::INFO::spectre.util.metadata.metadataCollector> Found No 48 N region: chr1:121955619-121955718
spectre::2024-04-08 10:11:59,267::INFO::spectre.util.metadata.metadataCollector> Found No 49 N region: chr1:121958015-121958114
spectre::2024-04-08 10:11:59,268::INFO::spectre.util.metadata.metadataCollector> Found No 50 N region: chr1:121963443-121963542
spectre::2024-04-08 10:11:59,268::INFO::spectre.util.metadata.metadataCollector> Found No 51 N region: chr1:121965833-121965932
spectre::2024-04-08 10:11:59,269::INFO::spectre.util.metadata.metadataCollector> Found No 52 N region: chr1:121968820-121968919
spectre::2024-04-08 10:11:59,269::INFO::spectre.util.metadata.metadataCollector> Found No 53 N region: chr1:121972191-121972290
spectre::2024-04-08 10:11:59,270::INFO::spectre.util.metadata.metadataCollector> Found No 54 N region: chr1:121974357-121974456
spectre::2024-04-08 10:11:59,274::INFO::spectre.util.metadata.metadataCollector> Found No 55 N region: chr1:121976459-122026458
spectre::2024-04-08 10:11:59,279::INFO::spectre.util.metadata.metadataCollector> Found No 56 N region: chr1:122056834-122056933
spectre::2024-04-08 10:11:59,286::INFO::spectre.util.metadata.metadataCollector> Found No 57 N region: chr1:122102991-122103090
spectre::2024-04-08 10:11:59,287::INFO::spectre.util.metadata.metadataCollector> Found No 58 N region: chr1:122109869-122109968
spectre::2024-04-08 10:11:59,289::INFO::spectre.util.metadata.metadataCollector> Found No 59 N region: chr1:122125244-122125343
spectre::2024-04-08 10:11:59,297::INFO::spectre.util.metadata.metadataCollector> Found No 60 N region: chr1:122173931-122174030
spectre::2024-04-08 10:11:59,305::INFO::spectre.util.metadata.metadataCollector> Found No 61 N region: chr1:122224535-122224634
spectre::2024-04-08 10:11:59,306::INFO::spectre.util.metadata.metadataCollector> Found No 62 N region: chr1:122229967-122230066
spectre::2024-04-08 10:11:59,307::INFO::spectre.util.metadata.metadataCollector> Found No 63 N region: chr1:122237366-122237465
spectre::2024-04-08 10:11:59,346::INFO::spectre.util.metadata.metadataCollector> Found No 64 N region: chr1:122503147-122503246
spectre::2024-04-08 10:11:59,689::INFO::spectre.util.metadata.metadataCollector> Found No 65 N region: chr1:124785432-124785531
spectre::2024-04-08 10:11:59,699::INFO::spectre.util.metadata.metadataCollector> Found No 66 N region: chr1:124849129-124849228
spectre::2024-04-08 10:11:59,712::INFO::spectre.util.metadata.metadataCollector> Found No 67 N region: chr1:124932724-124932823
spectre::2024-04-08 10:11:59,719::INFO::spectre.util.metadata.metadataCollector> Found No 68 N region: chr1:124977944-124978325
spectre::2024-04-08 10:11:59,724::INFO::spectre.util.metadata.metadataCollector> Found No 69 N region: chr1:125013060-125013222
spectre::2024-04-08 10:11:59,726::INFO::spectre.util.metadata.metadataCollector> Found No 70 N region: chr1:125026048-125026070
spectre::2024-04-08 10:11:59,727::INFO::spectre.util.metadata.metadataCollector> Found No 71 N region: chr1:125029104-125029168
spectre::2024-04-08 10:11:59,738::INFO::spectre.util.metadata.metadataCollector> Found No 72 N region: chr1:125103213-125103232
spectre::2024-04-08 10:11:59,742::INFO::spectre.util.metadata.metadataCollector> Found No 73 N region: chr1:125130246-125131846
spectre::2024-04-08 10:11:59,749::INFO::spectre.util.metadata.metadataCollector> Found No 74 N region: chr1:125171347-125173582
spectre::2024-04-08 10:12:01,160::INFO::spectre.util.metadata.metadataCollector> Found No 75 N region: chr1:125184587-143184586
spectre::2024-04-08 10:12:13,492::INFO::spectre.util.metadata.metadataCollector> Found No 76 N region: chr1:223558935-223608934
spectre::2024-04-08 10:12:14,240::INFO::spectre.util.metadata.metadataCollector> Found No 77 N region: chr1:228558364-228608363
[...]
spectre::2024-04-08 10:19:18,360::INFO::spectre.util.metadata.metadataCollector> Reading >chrY
spectre::2024-04-08 10:19:18,361::INFO::spectre.util.metadata.metadataCollector> Found No 1 N region: chrY:1-9999
spectre::2024-04-08 10:19:18,370::INFO::spectre.util.metadata.metadataCollector> Found No 2 N region: chrY:44821-94820
spectre::2024-04-08 10:19:18,383::INFO::spectre.util.metadata.metadataCollector> Found No 3 N region: chrY:133871-222345
spectre::2024-04-08 10:19:18,384::INFO::spectre.util.metadata.metadataCollector> Found No 4 N region: chrY:226276-226350
spectre::2024-04-08 10:19:18,654::INFO::spectre.util.metadata.metadataCollector> Found No 5 N region: chrY:1949345-2132993
spectre::2024-04-08 10:19:18,655::INFO::spectre.util.metadata.metadataCollector> Found No 6 N region: chrY:2137388-2137487
spectre::2024-04-08 10:19:19,689::INFO::spectre.util.metadata.metadataCollector> Found No 7 N region: chrY:9046914-9055173
spectre::2024-04-08 10:19:19,694::INFO::spectre.util.metadata.metadataCollector> Found No 8 N region: chrY:9057608-9107607
spectre::2024-04-08 10:19:19,695::INFO::spectre.util.metadata.metadataCollector> Found No 9 N region: chrY:9111868-9112714
spectre::2024-04-08 10:19:19,695::INFO::spectre.util.metadata.metadataCollector> Found No 10 N region: chrY:9114319-9116370
spectre::2024-04-08 10:19:19,742::INFO::spectre.util.metadata.metadataCollector> Found No 11 N region: chrY:9403713-9453712
spectre::2024-04-08 10:19:19,867::INFO::spectre.util.metadata.metadataCollector> Found No 12 N region: chrY:10266944-10316943
spectre::2024-04-08 10:19:19,906::INFO::spectre.util.metadata.metadataCollector> Found No 13 N region: chrY:10544039-10594038
spectre::2024-04-08 10:19:19,914::INFO::spectre.util.metadata.metadataCollector> Found No 14 N region: chrY:10633440-10645832
spectre::2024-04-08 10:19:19,915::INFO::spectre.util.metadata.metadataCollector> Found No 15 N region: chrY:10649989-10651420
spectre::2024-04-08 10:19:19,918::INFO::spectre.util.metadata.metadataCollector> Found No 16 N region: chrY:10669737-10670731
spectre::2024-04-08 10:19:19,919::INFO::spectre.util.metadata.metadataCollector> Found No 17 N region: chrY:10674058-10676543
spectre::2024-04-08 10:19:19,920::INFO::spectre.util.metadata.metadataCollector> Found No 18 N region: chrY:10679715-10682441
spectre::2024-04-08 10:19:19,921::INFO::spectre.util.metadata.metadataCollector> Found No 19 N region: chrY:10691573-10691901
spectre::2024-04-08 10:19:19,927::INFO::spectre.util.metadata.metadataCollector> Found No 20 N region: chrY:10694192-10744191
spectre::2024-04-08 10:19:19,928::INFO::spectre.util.metadata.metadataCollector> Found No 21 N region: chrY:10747280-10747304
spectre::2024-04-08 10:19:19,940::INFO::spectre.util.metadata.metadataCollector> Found No 22 N region: chrY:10809671-10810478
spectre::2024-04-08 10:19:19,942::INFO::spectre.util.metadata.metadataCollector> Found No 23 N region: chrY:10816758-10817291
spectre::2024-04-08 10:19:19,949::INFO::spectre.util.metadata.metadataCollector> Found No 24 N region: chrY:10852900-10855134
spectre::2024-04-08 10:19:19,952::INFO::spectre.util.metadata.metadataCollector> Found No 25 N region: chrY:10871218-10871896
spectre::2024-04-08 10:19:19,956::INFO::spectre.util.metadata.metadataCollector> Found No 26 N region: chrY:10890419-10891941
spectre::2024-04-08 10:19:19,957::INFO::spectre.util.metadata.metadataCollector> Found No 27 N region: chrY:10896525-10898183
spectre::2024-04-08 10:19:19,961::INFO::spectre.util.metadata.metadataCollector> Found No 28 N region: chrY:10908519-10909100
spectre::2024-04-08 10:19:19,965::INFO::spectre.util.metadata.metadataCollector> Found No 29 N region: chrY:10922486-10923563
spectre::2024-04-08 10:19:19,988::INFO::spectre.util.metadata.metadataCollector> Found No 30 N region: chrY:10956868-10957766
spectre::2024-04-08 10:19:19,989::INFO::spectre.util.metadata.metadataCollector> Found No 31 N region: chrY:10961625-10962532
spectre::2024-04-08 10:19:19,990::INFO::spectre.util.metadata.metadataCollector> Found No 32 N region: chrY:10965694-10967283
spectre::2024-04-08 10:19:19,990::INFO::spectre.util.metadata.metadataCollector> Found No 33 N region: chrY:10969992-10970619
spectre::2024-04-08 10:19:19,993::INFO::spectre.util.metadata.metadataCollector> Found No 34 N region: chrY:10986652-10986676
spectre::2024-04-08 10:19:19,996::INFO::spectre.util.metadata.metadataCollector> Found No 35 N region: chrY:11002276-11003058
spectre::2024-04-08 10:19:19,998::INFO::spectre.util.metadata.metadataCollector> Found No 36 N region: chrY:11012528-11013045
spectre::2024-04-08 10:19:19,999::INFO::spectre.util.metadata.metadataCollector> Found No 37 N region: chrY:11016992-11017246
spectre::2024-04-08 10:19:20,000::INFO::spectre.util.metadata.metadataCollector> Found No 38 N region: chrY:11023374-11024265
spectre::2024-04-08 10:19:20,001::INFO::spectre.util.metadata.metadataCollector> Found No 39 N region: chrY:11028342-11029159
spectre::2024-04-08 10:19:20,002::INFO::spectre.util.metadata.metadataCollector> Found No 40 N region: chrY:11036252-11037031
spectre::2024-04-08 10:19:20,093::INFO::spectre.util.metadata.metadataCollector> Found No 41 N region: chrY:11592902-11642901
spectre::2024-04-08 10:19:20,094::INFO::spectre.util.metadata.metadataCollector> Found No 42 N region: chrY:11647442-11647708
spectre::2024-04-08 10:19:20,095::INFO::spectre.util.metadata.metadataCollector> Found No 43 N region: chrY:11653064-11653101
spectre::2024-04-08 10:19:20,097::INFO::spectre.util.metadata.metadataCollector> Found No 44 N region: chrY:11660374-11662180
spectre::2024-04-08 10:19:20,097::INFO::spectre.util.metadata.metadataCollector> Found No 45 N region: chrY:11663986-11664005
spectre::2024-04-08 10:19:20,098::INFO::spectre.util.metadata.metadataCollector> Found No 46 N region: chrY:11669948-11670087
spectre::2024-04-08 10:19:20,098::INFO::spectre.util.metadata.metadataCollector> Found No 47 N region: chrY:11671800-11671819
spectre::2024-04-08 10:19:20,099::INFO::spectre.util.metadata.metadataCollector> Found No 48 N region: chrY:11673795-11674122
spectre::2024-04-08 10:19:21,449::INFO::spectre.util.metadata.metadataCollector> Found No 49 N region: chrY:20207793-20257792
spectre::2024-04-08 10:19:21,670::INFO::spectre.util.metadata.metadataCollector> Found No 50 N region: chrY:21739542-21741440
spectre::2024-04-08 10:19:21,671::INFO::spectre.util.metadata.metadataCollector> Found No 51 N region: chrY:21747863-21748370
spectre::2024-04-08 10:19:21,672::INFO::spectre.util.metadata.metadataCollector> Found No 52 N region: chrY:21750013-21750313
spectre::2024-04-08 10:19:21,679::INFO::spectre.util.metadata.metadataCollector> Found No 53 N region: chrY:21789281-21805280
spectre::2024-04-08 10:19:24,724::INFO::spectre.util.metadata.metadataCollector> Found No 54 N region: chrY:26673214-56673213
spectre::2024-04-08 10:19:24,743::INFO::spectre.util.metadata.metadataCollector> Found No 55 N region: chrY:56771509-56821508
spectre::2024-04-08 10:19:24,802::INFO::spectre.util.metadata.metadataCollector> Calculating bp statistics
spectre::2024-04-08 10:19:24,802::INFO::spectre.util.metadata.metadataCollector> Calculating N positions
spectre::2024-04-08 10:19:24,803::INFO::spectre.util.metadata.metadataCollector> Writing report
spectre::2024-04-08 10:19:24,803::INFO::spectre.util.metadata.metadataCollector> Writing MDR to: /srv/scratch/testardqu/tickets/28452/Spectre/results_test/metadata.mdr
spectre::2024-04-08 10:19:24,807::DEBUG::spectre.spectre> genome: ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chr6', 'chr7', 'chr8', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr20', 'chr21', 'chr22', 'chrX', 'chrY']
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/usr/local/lib/python3.11/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/multiprocessing/pool.py", line 48, in mapstar
return list(map(*args))
^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/spectre/spectre.py", line 142, in outside_spectre_worker
coverage_filepath=si["coverage_filepath"], sample_id=si["sample_id"],
~~^^^^^^^^^^^^^^^^^^^^^
KeyError: 'coverage_filepath'
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/local/bin/spectre", line 8, in <module>
sys.exit(main())
^^^^^^
File "/usr/local/lib/python3.11/site-packages/spectre/spectre.py", line 614, in main
spectre_run.spectre_exe()
File "/usr/local/lib/python3.11/site-packages/spectre/spectre.py", line 337, in spectre_exe
results = pool.map(outside_spectre_worker, tuple(spectre_instructions))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/multiprocessing/pool.py", line 367, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/multiprocessing/pool.py", line 774, in get
raise self._value
KeyError: 'coverage_filepath'Without the --population parameter, the tool runs, but only produces results for the first patient in the order. For the moment, I'm getting by with a shell for loop that swaps the first patient at each iteration.
I don't know if this is a bug or just me misunderstanding the purpose of this parameter.
Regards.
Empty vcf file produced instead of vcf.gz file
Hello,
I noticed that for some samples in my cohort, the final files produced were empty vcf files instead of vcf.gz files when these included CNVs. Is this the expected behavior when simply no CNV is called ?
There don't seem to be any errors in the logs.
Sample1
├── Sample1.spc.gz
├── Sample1.vcf
├── Sample1_cnv.bed.gz
├── Sample1_cnv.bed.gz.tbi
├── debug
│ ├── cnv_Sample1_byCoverage_chrchr1.csv
│ ├── cnv_Sample1_byCoverage_chrchr10.csv
│ ├── cnv_Sample1_byCoverage_chrchr11.csv
│ ├── cnv_Sample1_byCoverage_chrchr12.csv
│ ├── cnv_Sample1_byCoverage_chrchr13.csv
│ ├── cnv_Sample1_byCoverage_chrchr14.csv
│ ├── cnv_Sample1_byCoverage_chrchr15.csv
│ ├── cnv_Sample1_byCoverage_chrchr16.csv
│ ├── cnv_Sample1_byCoverage_chrchr17.csv
│ ├── cnv_Sample1_byCoverage_chrchr18.csv
│ ├── cnv_Sample1_byCoverage_chrchr19.csv
│ ├── cnv_Sample1_byCoverage_chrchr2.csv
│ ├── cnv_Sample1_byCoverage_chrchr20.csv
│ ├── cnv_Sample1_byCoverage_chrchr21.csv
│ ├── cnv_Sample1_byCoverage_chrchr22.csv
│ ├── cnv_Sample1_byCoverage_chrchr3.csv
│ ├── cnv_Sample1_byCoverage_chrchr4.csv
│ ├── cnv_Sample1_byCoverage_chrchr5.csv
│ ├── cnv_Sample1_byCoverage_chrchr6.csv
│ ├── cnv_Sample1_byCoverage_chrchr7.csv
│ ├── cnv_Sample1_byCoverage_chrchr8.csv
│ ├── cnv_Sample1_byCoverage_chrchr9.csv
│ ├── cnv_Sample1_byCoverage_chrchrX.csv
│ ├── cnv_metrics_random_samples.csv.gz
│ ├── genome_coverage_distribution-Sample1.png
│ ├── raw-cnvsSample1.bed.gz
│ └── raw-cnvsSample1.bed.gz.tbi
├── img
│ ├── Sample1_plot_cnv_chr1.png
│ ├── Sample1_plot_cnv_chr10.png
│ ├── Sample1_plot_cnv_chr11.png
│ ├── Sample1_plot_cnv_chr12.png
│ ├── Sample1_plot_cnv_chr13.png
│ ├── Sample1_plot_cnv_chr14.png
│ ├── Sample1_plot_cnv_chr15.png
│ ├── Sample1_plot_cnv_chr16.png
│ ├── Sample1_plot_cnv_chr17.png
│ ├── Sample1_plot_cnv_chr18.png
│ ├── Sample1_plot_cnv_chr19.png
│ ├── Sample1_plot_cnv_chr2.png
│ ├── Sample1_plot_cnv_chr20.png
│ ├── Sample1_plot_cnv_chr21.png
│ ├── Sample1_plot_cnv_chr22.png
│ ├── Sample1_plot_cnv_chr3.png
│ ├── Sample1_plot_cnv_chr4.png
│ ├── Sample1_plot_cnv_chr5.png
│ ├── Sample1_plot_cnv_chr6.png
│ ├── Sample1_plot_cnv_chr7.png
│ ├── Sample1_plot_cnv_chr8.png
│ ├── Sample1_plot_cnv_chr9.png
│ └── Sample1_plot_cnv_chrX.png
├── metadata.mdr -> /srv/scratch/testardqu/tickets/28452/Spectre/metadata.mdr
└── tmp
3 directories, 55 filesSample2/
├── Sample2.spc.gz
├── Sample2.vcf.gz
├── Sample2.vcf.gz.tbi
├── Sample2_cnv.bed.gz
├── Sample2_cnv.bed.gz.tbi
├── debug
│ ├── cnv_Sample2_byCoverage_chrchr1.csv
│ ├── cnv_Sample2_byCoverage_chrchr10.csv
│ ├── cnv_Sample2_byCoverage_chrchr11.csv
│ ├── cnv_Sample2_byCoverage_chrchr12.csv
│ ├── cnv_Sample2_byCoverage_chrchr13.csv
│ ├── cnv_Sample2_byCoverage_chrchr14.csv
│ ├── cnv_Sample2_byCoverage_chrchr15.csv
│ ├── cnv_Sample2_byCoverage_chrchr16.csv
│ ├── cnv_Sample2_byCoverage_chrchr17.csv
│ ├── cnv_Sample2_byCoverage_chrchr18.csv
│ ├── cnv_Sample2_byCoverage_chrchr19.csv
│ ├── cnv_Sample2_byCoverage_chrchr2.csv
│ ├── cnv_Sample2_byCoverage_chrchr20.csv
│ ├── cnv_Sample2_byCoverage_chrchr21.csv
│ ├── cnv_Sample2_byCoverage_chrchr22.csv
│ ├── cnv_Sample2_byCoverage_chrchr3.csv
│ ├── cnv_Sample2_byCoverage_chrchr4.csv
│ ├── cnv_Sample2_byCoverage_chrchr5.csv
│ ├── cnv_Sample2_byCoverage_chrchr6.csv
│ ├── cnv_Sample2_byCoverage_chrchr7.csv
│ ├── cnv_Sample2_byCoverage_chrchr8.csv
│ ├── cnv_Sample2_byCoverage_chrchr9.csv
│ ├── cnv_Sample2_byCoverage_chrchrX.csv
│ ├── cnv_metrics_random_samples.csv.gz
│ ├── genome_coverage_distribution-Sample2.png
│ ├── raw-cnvsSample2.bed.gz
│ └── raw-cnvsSample2.bed.gz.tbi
├── img
│ ├── Sample2_plot_cnv_chr1.png
│ ├── Sample2_plot_cnv_chr10.png
│ ├── Sample2_plot_cnv_chr11.png
│ ├── Sample2_plot_cnv_chr12.png
│ ├── Sample2_plot_cnv_chr13.png
│ ├── Sample2_plot_cnv_chr14.png
│ ├── Sample2_plot_cnv_chr15.png
│ ├── Sample2_plot_cnv_chr16.png
│ ├── Sample2_plot_cnv_chr17.png
│ ├── Sample2_plot_cnv_chr18.png
│ ├── Sample2_plot_cnv_chr19.png
│ ├── Sample2_plot_cnv_chr2.png
│ ├── Sample2_plot_cnv_chr20.png
│ ├── Sample2_plot_cnv_chr21.png
│ ├── Sample2_plot_cnv_chr22.png
│ ├── Sample2_plot_cnv_chr3.png
│ ├── Sample2_plot_cnv_chr4.png
│ ├── Sample2_plot_cnv_chr5.png
│ ├── Sample2_plot_cnv_chr6.png
│ ├── Sample2_plot_cnv_chr7.png
│ ├── Sample2_plot_cnv_chr8.png
│ ├── Sample2_plot_cnv_chr9.png
│ └── Sample2_plot_cnv_chrX.png
├── metadata.mdr -> /srv/scratch/testardqu/tickets/28452/Spectre/metadata.mdr
└── tmp
3 directories, 56 fileszgrep -vc "#" Sample2/Sample2.vcf.gz
18
grep -vc "#" Sample1/Sample1.vcf
1There is a blank line at the end of the vcf file.
Thanks.
RecursionError: maximum recursion depth exceeded in comparison
Hi team
Command used:
spectre CNVCaller --coverage mosdepth/"$A".regions.bed.gz --sample-id $A --output-dir spectre2 --reference ~/beggsa-clinicalnanopore/genomes/grch38/genome.fa --metadata ~/beggsa-clinicalnanopore/genomes/grch38/grch38spectremetadata.mdr --blacklist ~/beggsa-clinicalnanopore/genomes/grch38/grch38_blacklist_spectre.bed --snv clair/merge_output.vcf.gz
Output:
spectre::2024-05-23 16:25:49,087::INFO::spectre.spectre> Spectre input: CNVCaller --coverage mosdepth/BRCA19.regions.bed.gz --sample-id BRCA19 --output-dir spectre2 --reference /rds/homes/b/beggsa/beggsa-clinicalnanopore/genomes/grch38/genome.fa --metadata /rds/homes/b/beggsa/beggsa-clinicalnanopore/genomes/grch38/grch38spectremetadata.mdr --blacklist /rds/homes/b/beggsa/beggsa-clinicalnanopore/genomes/grch38/grch38_blacklist_spectre.bed --snv clair/merge_output.vcf.gz
spectre::2024-05-23 16:25:49,088::INFO::spectre.spectre> Spectre version: 0.2.1
spectre::2024-05-23 16:25:49,088::INFO::spectre.spectre> Starting spectre
spectre::2024-05-23 16:25:49,088::INFO::spectre.spectre> Evaluate if a new .mdr file needs to be created
spectre::2024-05-23 16:25:49,118::INFO::spectre.spectre> Using existing metadata file /rds/homes/b/beggsa/beggsa-clinicalnanopore/genomes/grch38/grch38spectremetadata.mdr
spectre::2024-05-23 16:25:49,207::INFO::spectre.spectreCNV> Spectre calculating for: mosdepth/BRCA19.regions.bed.gz
spectre::2024-05-23 16:25:49,231::INFO::spectre.spectreCNV> Analysing CN neutral state from SNV data
spectre::2024-05-23 16:25:49,417::DEBUG::spectre.analysis.snv_analysis> Starting SNV Copy number state compute ...
spectre::2024-05-23 16:25:49,417::DEBUG::spectre.analysis.snv_analysis> Het sites count per chromosome
spectre::2024-05-23 16:26:11,222::DEBUG::spectre.analysis.snv_analysis> chr1 348064 34372 35735 5.61x 49.03% het pass | 9.88% het all
spectre::2024-05-23 16:26:11,224::DEBUG::spectre.analysis.snv_analysis> chr2 360835 35100 34955 5.03x 50.1% het pass | 9.73% het all
spectre::2024-05-23 16:26:11,224::DEBUG::spectre.analysis.snv_analysis> chr3 301628 29810 29345 5.0x 50.39% het pass | 9.88% het all
spectre::2024-05-23 16:26:11,224::DEBUG::spectre.analysis.snv_analysis> chr4 311748 29295 34509 5.74x 45.91% het pass | 9.4% het all
spectre::2024-05-23 16:26:11,224::DEBUG::spectre.analysis.snv_analysis> chr5 267189 26028 25446 5.31x 50.57% het pass | 9.74% het all
spectre::2024-05-23 16:26:11,224::DEBUG::spectre.analysis.snv_analysis> chr6 267229 26282 26283 4.84x 50.0% het pass | 9.84% het all
spectre::2024-05-23 16:26:11,224::DEBUG::spectre.analysis.snv_analysis> chr7 244566 25388 24447 5.03x 50.94% het pass | 10.38% het all
spectre::2024-05-23 16:26:11,224::DEBUG::spectre.analysis.snv_analysis> chr8 222152 21960 21678 4.93x 50.32% het pass | 9.89% het all
spectre::2024-05-23 16:26:11,224::DEBUG::spectre.analysis.snv_analysis> chr9 185783 19339 17906 5.21x 51.92% het pass | 10.41% het all
spectre::2024-05-23 16:26:11,224::DEBUG::spectre.analysis.snv_analysis> chr10 210841 21484 20617 5.78x 51.03% het pass | 10.19% het all
spectre::2024-05-23 16:26:11,224::DEBUG::spectre.analysis.snv_analysis> chr11 214518 20288 23947 4.91x 45.86% het pass | 9.46% het all
spectre::2024-05-23 16:26:11,224::DEBUG::spectre.analysis.snv_analysis> chr12 203810 19444 20429 4.89x 48.76% het pass | 9.54% het all
spectre::2024-05-23 16:26:11,224::DEBUG::spectre.analysis.snv_analysis> chr13 166597 15197 20132 5.5x 43.02% het pass | 9.12% het all
spectre::2024-05-23 16:26:11,224::DEBUG::spectre.analysis.snv_analysis> chr14 139807 13814 14842 5.15x 48.21% het pass | 9.88% het all
spectre::2024-05-23 16:26:11,224::DEBUG::spectre.analysis.snv_analysis> chr15 124321 12076 12731 4.95x 48.68% het pass | 9.71% het all
spectre::2024-05-23 16:26:11,224::DEBUG::spectre.analysis.snv_analysis> chr16 125786 13380 12426 7.2x 51.85% het pass | 10.64% het all
spectre::2024-05-23 16:26:11,224::DEBUG::spectre.analysis.snv_analysis> chr17 116927 12944 11131 5.76x 53.77% het pass | 11.07% het all
spectre::2024-05-23 16:26:11,225::DEBUG::spectre.analysis.snv_analysis> chr18 124000 11796 13121 5.28x 47.34% het pass | 9.51% het all
spectre::2024-05-23 16:26:11,228::DEBUG::spectre.analysis.snv_analysis> chr19 86274 9538 7477 5.33x 56.06% het pass | 11.06% het all
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis> chr20 106365 14681 8842 6.65x 62.41% het pass | 13.8% het all
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis> chr21 68940 9203 7310 7.39x 55.73% het pass | 13.35% het all
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis> chr22 62161 8543 5257 6.61x 61.91% het pass | 13.74% het all
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis> chrX 183860 16011 14272 4.77x 52.87% het pass | 8.71% het all
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis> chrY 5266 815 1541 19.96x 34.59% het pass | 15.48% het all
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis> Use chromsomes based on proportion of het sites
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis> chr1 5.61
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis> chr2 5.03
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis> chr3 5.0
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis> chr4 5.74
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis> chr5 5.31
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis> chr6 4.84
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis> chr7 5.03
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis> chr8 4.93
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis> chr9 5.21
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis> chr10 5.78
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis> chr11 4.91
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis> chr12 4.89
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis> chr13 5.5
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis> chr14 5.15
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis> chr15 4.95
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis> chr16 7.2
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis> chr17 5.76
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis> chr18 5.28
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis> chr19 5.33
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis> chr20 6.65
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis> chr21 7.39
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis> chr22 6.61
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis> chrX 4.77
spectre::2024-05-23 16:26:33,908::DEBUG::spectre.analysis.snv_analysis> n het sites used for normalization = 1174573
spectre::2024-05-23 16:26:34,094::DEBUG::spectre.analysis.snv_analysis> p98 HET filter = 8.0
spectre::2024-05-23 16:26:34,643::DEBUG::spectre.analysis.snv_analysis> HET: 1174573 | p98 HET 1153663
Traceback (most recent call last):
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/bin/spectre", line 8, in <module>
sys.exit(main())
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/spectre/spectre.py", line 642, in main
spectre_run.spectre_exe()
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/spectre/spectre.py", line 356, in spectre_exe
spectre_main.cnv_call()
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/spectre/spectreCNV.py", line 71, in cnv_call
self.snv_analysis.snv_copy_number_state()
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/spectre/analysis/snv_analysis.py", line 231, in snv_copy_number_state
self.snv_multimodal_detect()
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/spectre/analysis/snv_analysis.py", line 106, in snv_multimodal_detect
dist_detected = detect_miltimodal.run()
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/spectre/libs/unidip/unidip.py", line 51, in run
modidxs = self._unidip(0, len(self.dat), True, self.debug)
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/spectre/libs/unidip/unidip.py", line 154, in _unidip
rhidx = self._unidip(start+h_idx[1], end, False, debug)
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/spectre/libs/unidip/unidip.py", line 154, in _unidip
rhidx = self._unidip(start+h_idx[1], end, False, debug)
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/spectre/libs/unidip/unidip.py", line 154, in _unidip
rhidx = self._unidip(start+h_idx[1], end, False, debug)
[Previous line repeated 975 more times]
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/spectre/libs/unidip/unidip.py", line 135, in _unidip
rmidx = self._unidip(start+modidx[0], start+modidx[1], True, debug)
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/spectre/libs/unidip/unidip.py", line 117, in _unidip
_, pval, modidx = diptst(dat, self.is_hist, self.ntrials)
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/spectre/libs/unidip/dip.py", line 55, in diptst
unif_dips = np.apply_along_axis(dip_fn, 1, unifs, is_hist, True)
File "<__array_function__ internals>", line 200, in apply_along_axis
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/numpy/lib/shape_base.py", line 379, in apply_along_axis
res = asanyarray(func1d(inarr_view[ind0], *args, **kwargs))
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/spectre/libs/unidip/dip.py", line 75, in dip_fn
counts = collections.Counter(dat)
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/collections/__init__.py", line 577, in __init__
self.update(iterable, **kwds)
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/collections/__init__.py", line 661, in update
if isinstance(iterable, _collections_abc.Mapping):
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/abc.py", line 119, in __instancecheck__
return _abc_instancecheck(cls, instance)
RecursionError: maximum recursion depth exceeded in comparison
Spectre needs a blacklist or crashes out
Hi team
Sorry to add another bug - if you run spectre0.2 without a blacklist implicitly supplied it gets to the CNV calling step and fails
A
Spectre error with UNK chromosome
Not really something extremely buggy, but currently with cattle we have a lot of unmapped chromosomes (NKLS02000...). These caused Spectre to fail (see below). Specifying --only-chr with numeric chromosome(s) will address the issue, but perhaps for a genome with "Chr01" it could also be potentially problematic.
spectre::INFO> refining cnv calls
/group/dairy/Tuan/Recessive_lethal/Long_read_seq_analysis/Spectre/Spectre/analysis/analysis.py:384: RuntimeWarning: invalid value encountered in scalar subtract
scaf_cov - np.nanmedian(list(_cand.cov) + list(_cand_next.cov))
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/group/home/vicsuwd/anaconda3/lib/python3.8/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/group/home/vicsuwd/anaconda3/lib/python3.8/multiprocessing/pool.py", line 48, in mapstar
return list(map(*args))
File "Spectre/spectre.py", line 117, in outside_spectre_worker
worker.cnv_call()
File "/group/dairy/Tuan/Recessive_lethal/Long_read_seq_analysis/Spectre/Spectre/spectreCNV.py", line 104, in cnv_call
self.cnv_analysis.refine_cnv_calls(self.as_dev) # set to self.as_dev
File "/group/dairy/Tuan/Recessive_lethal/Long_read_seq_analysis/Spectre/Spectre/analysis/analysis.py", line 273, in refine_cnv_calls
final_cnv_candidates = self.merge_candidates(candidates_cnv_list, each_chromosome)
File "/group/dairy/Tuan/Recessive_lethal/Long_read_seq_analysis/Spectre/Spectre/analysis/analysis.py", line 285, in merge_candidates
[n_merges, merged_candidates, _] = self.cnv_candidate_merge(candidates_cnv_list)
File "/group/dairy/Tuan/Recessive_lethal/Long_read_seq_analysis/Spectre/Spectre/analysis/analysis.py", line 333, in cnv_candidate_merge
any(end0 <= int(val) <= start1 for val in tup) for tup in self.metadata[cnv_cand.chromosome])
KeyError: 'NKLS02000880.1'
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "Spectre/spectre.py", line 500, in <module>
main()
File "Spectre/spectre.py", line 482, in main
spectre_run.spectre_exe()
File "Spectre/spectre.py", line 256, in spectre_exe
results = pool.map(outside_spectre_worker, tuple(spectre_instructions))
File "/group/home/vicsuwd/anaconda3/lib/python3.8/multiprocessing/pool.py", line 364, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/group/home/vicsuwd/anaconda3/lib/python3.8/multiprocessing/pool.py", line 771, in get
raise self._value
KeyError: 'NKLS02000880.1'```
False positives CNV called for chrX in men
Hello,
I did the CNV call one by one on my cohort of 26 samples. Of all the CNVs called, 253 out of 254 were on the X chromosome. All of these CNVs were called in males (although the cohort is almost equally made up of males and females).
However, I think I've used the --ploidy-chr parameter correctly, see exemple command below.
singularity exec --bind /srv:/srv spectre.0.2.0.sif spectre CNVCaller \
--coverage mosdepth/Sample1.regions.bed.gz mosdepth/Sample2.regions.bed.gz mosdepth/Sample3.regions.bed.gz mosdepth/Sample4.regions.bed.gz mosdepth/Sample5.regions.bed.gz mosdepth/Sample6.regions.bed.gz mosdepth/Sample7.regions.bed.gz mosdepth/Sample8.regions.bed.gz mosdepth/Sample9.regions.bed.gz mosdepth/Sample10.regions.bed.gz mosdepth/Sample11.regions.bed.gz mosdepth/Sample12.regions.bed.gz mosdepth/Sample13.regions.bed.gz mosdepth/Sample14.regions.bed.gz mosdepth/Sample15.regions.bed.gz mosdepth/Sample16.regions.bed.gz mosdepth/Sample17.regions.bed.gz mosdepth/Sample18.regions.bed.gz mosdepth/Sample19.regions.bed.gz mosdepth/Sample20.regions.bed.gz mosdepth/Sample21.regions.bed.gz mosdepth/Sample22.regions.bed.gz mosdepth/Sample23.regions.bed.gz mosdepth/Sample24.regions.bed.gz mosdepth/Sample25.regions.bed.gz mosdepth/Sample26.regions.bed.gz \
--sample-id Sample1 Sample2 Sample3 Sample4 Sample5 Sample6 Sample7 Sample8 Sample9 Sample10 Sample11 Sample12 Sample13 Sample14 Sample15 Sample16 Sample17 Sample18 Sample19 Sample20 Sample21 Sample22 Sample23 Sample24 Sample25 Sample26 \
--output-dir results/Sample1/ \
--blacklist grch38_blacklist_spectre.bed \
--only-chr chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY \
-0 \
--ploidy-chr chrX:1,chrY:1 \
--reference GRCh38.p13.canonical.fa.gz Most of the CNVs called are deletions and have recurrent coordinates.
Here is the CNV called by Spectre :
Sample4 chrX 4002000 END=8605000;SVLEN=4603000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample25 chrX 4002000 END=31062000;SVLEN=27060000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.52
Sample17 chrX 4002000 END=31075000;SVLEN=27073000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.5
Sample21 chrX 4002000 END=31075000;SVLEN=27073000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.5
Sample10 chrX 4002000 END=31075000;SVLEN=27073000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample23 chrX 4002000 END=31075000;SVLEN=27073000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample24 chrX 4002000 END=31080000;SVLEN=27078000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.51
Sample19 chrX 4002000 END=31085000;SVLEN=27083000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.5
Sample12 chrX 4002000 END=31110000;SVLEN=27108000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.5
Sample5 chrX 4002000 END=31130000;SVLEN=27128000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.5
Sample16 chrX 4002000 END=31474000;SVLEN=27472000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.53
Sample13 chrX 4002000 END=31851000;SVLEN=27849000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.53
Sample8 chrX 4002000 END=36999000;SVLEN=32997000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.53
Sample14 chrX 4002000 END=36999000;SVLEN=32997000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.52
Sample15 chrX 4002000 END=36999000;SVLEN=32997000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.52
Sample4 chrX 8638000 END=31092000;SVLEN=22454000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample16 chrX 31069000 END=33362000;SVLEN=2293000;SVTYPE=DUP;CN=4;SVSUPPORT=FALSE 1/1:0:0:4.02
Sample10 chrX 31083000 END=36999000;SVLEN=5916000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.63
Sample17 chrX 31089000 END=36999000;SVLEN=5910000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.62
Sample13 chrX 31862000 END=33353000;SVLEN=1491000;SVTYPE=DUP;CN=5;SVSUPPORT=FALSE ./.:0:0:4.65
Sample19 chrX 33331000 END=36999000;SVLEN=3668000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample12 chrX 33342000 END=36999000;SVLEN=3657000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.49
Sample23 chrX 33342000 END=36999000;SVLEN=3657000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample4 chrX 33354000 END=36999000;SVLEN=3645000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.53
Sample25 chrX 33359000 END=36999000;SVLEN=3640000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.52
Sample16 chrX 33359000 END=36999000;SVLEN=3640000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.54
Sample13 chrX 33362000 END=36999000;SVLEN=3637000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.49
Sample5 chrX 33362000 END=36999000;SVLEN=3637000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample24 chrX 33363000 END=36999000;SVLEN=3636000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.53
Sample21 chrX 33365000 END=36999000;SVLEN=3634000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample23 chrX 38001000 END=40030000;SVLEN=2029000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample4 chrX 38001000 END=40030000;SVLEN=2029000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.48
Sample5 chrX 38001000 END=40035000;SVLEN=2034000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample12 chrX 38001000 END=40040000;SVLEN=2039000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample21 chrX 38001000 END=40061000;SVLEN=2060000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample19 chrX 38001000 END=40110000;SVLEN=2109000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample24 chrX 38001000 END=40114000;SVLEN=2113000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.48
Sample8 chrX 38401000 END=40026000;SVLEN=1625000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.49
Sample25 chrX 38401000 END=40046000;SVLEN=1645000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample17 chrX 38425000 END=40060000;SVLEN=1635000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample10 chrX 38443000 END=40023000;SVLEN=1580000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.5
Sample16 chrX 38445000 END=40025000;SVLEN=1580000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.54
Sample14 chrX 38445000 END=40030000;SVLEN=1585000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample15 chrX 38446000 END=40026000;SVLEN=1580000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample13 chrX 38450000 END=40019000;SVLEN=1569000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.47
Sample25 chrX 40154000 END=48619000;SVLEN=8465000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.52
Sample12 chrX 40169000 END=49199000;SVLEN=9030000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample23 chrX 40178000 END=48766000;SVLEN=8588000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample17 chrX 40179000 END=48684000;SVLEN=8505000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.5
Sample10 chrX 40192000 END=48517000;SVLEN=8325000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample15 chrX 40194000 END=48759000;SVLEN=8565000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample19 chrX 40196000 END=48766000;SVLEN=8570000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample16 chrX 40198000 END=48249000;SVLEN=8051000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.53
Sample14 chrX 40198000 END=48593000;SVLEN=8395000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample5 chrX 40199000 END=48766000;SVLEN=8567000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample24 chrX 40199000 END=48771000;SVLEN=8572000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.5
Sample13 chrX 40200000 END=48760000;SVLEN=8560000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.47
Sample4 chrX 40201000 END=48760000;SVLEN=8559000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample8 chrX 40201000 END=48786000;SVLEN=8585000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.5
Sample21 chrX 40202000 END=48782000;SVLEN=8580000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample10 chrX 50401000 END=51999000;SVLEN=1598000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.5
Sample17 chrX 50401000 END=51999000;SVLEN=1598000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.5
Sample19 chrX 50401000 END=51999000;SVLEN=1598000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.5
Sample21 chrX 50401000 END=51999000;SVLEN=1598000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.5
Sample24 chrX 50401000 END=51999000;SVLEN=1598000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.5
Sample13 chrX 50401000 END=51999000;SVLEN=1598000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.48
Sample15 chrX 50401000 END=51999000;SVLEN=1598000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.49
Sample12 chrX 50401000 END=51999000;SVLEN=1598000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample23 chrX 50401000 END=51999000;SVLEN=1598000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample4 chrX 50401000 END=51999000;SVLEN=1598000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample8 chrX 50401000 END=51999000;SVLEN=1598000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample14 chrX 50401000 END=51999000;SVLEN=1598000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample16 chrX 50401000 END=51999000;SVLEN=1598000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample25 chrX 50401000 END=51999000;SVLEN=1598000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample5 chrX 50401000 END=51999000;SVLEN=1598000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample10 chrX 53001000 END=55399000;SVLEN=2398000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.5
Sample5 chrX 53001000 END=55399000;SVLEN=2398000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.5
Sample19 chrX 53001000 END=55399000;SVLEN=2398000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample23 chrX 53001000 END=55399000;SVLEN=2398000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample8 chrX 53001000 END=55603000;SVLEN=2602000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample13 chrX 53001000 END=55607000;SVLEN=2606000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.46
Sample16 chrX 53001000 END=55617000;SVLEN=2616000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.52
Sample24 chrX 53001000 END=55627000;SVLEN=2626000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.49
Sample15 chrX 53001000 END=55632000;SVLEN=2631000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.49
Sample25 chrX 53001000 END=55659000;SVLEN=2658000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample4 chrX 53001000 END=55692000;SVLEN=2691000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.49
Sample12 chrX 53001000 END=55772000;SVLEN=2771000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.5
Sample17 chrX 53001000 END=55812000;SVLEN=2811000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample14 chrX 53001000 END=55852000;SVLEN=2851000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample21 chrX 53001000 END=57999000;SVLEN=4998000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample8 chrX 55076000 END=57999000;SVLEN=2923000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.52
Sample16 chrX 55092000 END=57999000;SVLEN=2907000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.54
Sample14 chrX 55097000 END=57999000;SVLEN=2902000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample15 chrX 55227000 END=57999000;SVLEN=2772000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample19 chrX 55242000 END=57999000;SVLEN=2757000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample4 chrX 55252000 END=57999000;SVLEN=2747000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.53
Sample5 chrX 55312000 END=57999000;SVLEN=2687000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample13 chrX 55389000 END=57999000;SVLEN=2610000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.48
Sample12 chrX 55601000 END=57999000;SVLEN=2398000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample17 chrX 55601000 END=57999000;SVLEN=2398000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample10 chrX 55601000 END=57999000;SVLEN=2398000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample23 chrX 55601000 END=57999000;SVLEN=2398000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample24 chrX 55601000 END=57999000;SVLEN=2398000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.52
Sample25 chrX 55611000 END=57992000;SVLEN=2381000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample21 chrX 63501000 END=71499000;SVLEN=7998000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample16 chrX 63501000 END=71499000;SVLEN=7998000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.53
Sample17 chrX 63501000 END=73007000;SVLEN=9506000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample14 chrX 63501000 END=73007000;SVLEN=9506000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample19 chrX 63501000 END=73007000;SVLEN=9506000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample24 chrX 63501000 END=73007000;SVLEN=9506000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample25 chrX 63501000 END=73007000;SVLEN=9506000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample5 chrX 63501000 END=73007000;SVLEN=9506000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample8 chrX 63501000 END=73022000;SVLEN=9521000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.52
Sample13 chrX 63501000 END=73057000;SVLEN=9556000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.47
Sample23 chrX 63501000 END=73057000;SVLEN=9556000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample10 chrX 63501000 END=73077000;SVLEN=9576000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample12 chrX 63501000 END=73082000;SVLEN=9581000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample4 chrX 63501000 END=73082000;SVLEN=9581000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample15 chrX 63501000 END=73257000;SVLEN=9756000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample4 chrX 70280000 END=101367000;SVLEN=31087000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.53
Sample15 chrX 70610000 END=101375000;SVLEN=30765000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample17 chrX 71250000 END=123865000;SVLEN=52615000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample16 chrX 71290000 END=101375000;SVLEN=30085000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.52
Sample24 chrX 71350000 END=101370000;SVLEN=30020000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.52
Sample25 chrX 71356000 END=101376000;SVLEN=30020000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.51
Sample8 chrX 71399000 END=101419000;SVLEN=30020000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.53
Sample14 chrX 71410000 END=101370000;SVLEN=29960000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample21 chrX 71415000 END=101369000;SVLEN=29954000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.5
Sample23 chrX 71419000 END=101389000;SVLEN=29970000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample5 chrX 71419000 END=101399000;SVLEN=29980000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample19 chrX 71420000 END=101375000;SVLEN=29955000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample13 chrX 71465000 END=80570000;SVLEN=9105000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.48
Sample10 chrX 71466000 END=101371000;SVLEN=29905000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.5
Sample12 chrX 71494000 END=101424000;SVLEN=29930000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.49
Sample13 chrX 80559000 END=101359000;SVLEN=20800000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample15 chrX 101432000 END=114199000;SVLEN=12767000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample14 chrX 101552000 END=116767000;SVLEN=15215000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.51
Sample10 chrX 101702000 END=114199000;SVLEN=12497000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample19 chrX 101832000 END=114199000;SVLEN=12367000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample12 chrX 101847000 END=114199000;SVLEN=12352000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.5
Sample8 chrX 102057000 END=116812000;SVLEN=14755000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.52
Sample16 chrX 102067000 END=116717000;SVLEN=14650000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.53
Sample21 chrX 102087000 END=114199000;SVLEN=12112000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample25 chrX 102128000 END=108843000;SVLEN=6715000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.51
Sample23 chrX 102167000 END=116752000;SVLEN=14585000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample13 chrX 102168000 END=116753000;SVLEN=14585000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.48
Sample5 chrX 102172000 END=116707000;SVLEN=14535000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample4 chrX 102182000 END=116722000;SVLEN=14540000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample24 chrX 102192000 END=114199000;SVLEN=12007000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample25 chrX 108296000 END=114192000;SVLEN=5896000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.51
Sample23 chrX 116701000 END=120849000;SVLEN=4148000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.5
Sample12 chrX 116701000 END=120849000;SVLEN=4148000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample21 chrX 116701000 END=120849000;SVLEN=4148000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample8 chrX 116701000 END=120849000;SVLEN=4148000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample24 chrX 116701000 END=121119000;SVLEN=4418000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample19 chrX 116701000 END=121129000;SVLEN=4428000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample16 chrX 116701000 END=121134000;SVLEN=4433000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.53
Sample14 chrX 116701000 END=121154000;SVLEN=4453000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.51
Sample15 chrX 116701000 END=121174000;SVLEN=4473000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample4 chrX 116701000 END=121234000;SVLEN=4533000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample10 chrX 116701000 END=121299000;SVLEN=4598000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample5 chrX 116701000 END=121314000;SVLEN=4613000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.5
Sample13 chrX 116711000 END=121267000;SVLEN=4556000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.47
Sample25 chrX 116711000 END=121647000;SVLEN=4936000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample14 chrX 120699000 END=123844000;SVLEN=3145000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample5 chrX 120708000 END=123843000;SVLEN=3135000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample21 chrX 120713000 END=123835000;SVLEN=3122000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.5
Sample13 chrX 120771000 END=123836000;SVLEN=3065000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.49
Sample24 chrX 120793000 END=123848000;SVLEN=3055000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.52
Sample25 chrX 120799000 END=123864000;SVLEN=3065000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.52
Sample10 chrX 120814000 END=123864000;SVLEN=3050000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.5
Sample16 chrX 120844000 END=123904000;SVLEN=3060000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.54
Sample8 chrX 120848000 END=123879000;SVLEN=3031000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.52
Sample15 chrX 121101000 END=123834000;SVLEN=2733000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.5
Sample19 chrX 121101000 END=123834000;SVLEN=2733000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample23 chrX 121101000 END=123839000;SVLEN=2738000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample12 chrX 121101000 END=123864000;SVLEN=2763000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.5
Sample4 chrX 121101000 END=123894000;SVLEN=2793000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.52
Sample19 chrX 124400000 END=129965000;SVLEN=5565000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample10 chrX 124425000 END=129954000;SVLEN=5529000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.49
Sample12 chrX 124429000 END=129969000;SVLEN=5540000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.49
Sample24 chrX 124429000 END=129974000;SVLEN=5545000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.52
Sample14 chrX 124434000 END=129959000;SVLEN=5525000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample5 chrX 124436000 END=129981000;SVLEN=5545000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample16 chrX 124437000 END=129957000;SVLEN=5520000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.53
Sample25 chrX 124439000 END=129974000;SVLEN=5535000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.52
Sample15 chrX 124440000 END=129955000;SVLEN=5515000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.5
Sample21 chrX 124441000 END=129981000;SVLEN=5540000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.5
Sample23 chrX 124442000 END=129967000;SVLEN=5525000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.5
Sample4 chrX 124446000 END=129976000;SVLEN=5530000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.53
Sample8 chrX 124447000 END=129977000;SVLEN=5530000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.53
Sample17 chrX 124449000 END=129974000;SVLEN=5525000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.5
Sample13 chrX 124465000 END=129950000;SVLEN=5485000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.49
Sample8 chrX 130027000 END=134352000;SVLEN=4325000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.52
Sample17 chrX 130063000 END=134403000;SVLEN=4340000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample10 chrX 130066000 END=134346000;SVLEN=4280000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample21 chrX 130076000 END=134381000;SVLEN=4305000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample24 chrX 130078000 END=134358000;SVLEN=4280000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample15 chrX 130079000 END=134349000;SVLEN=4270000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample19 chrX 130079000 END=134349000;SVLEN=4270000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample4 chrX 130080000 END=134350000;SVLEN=4270000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample5 chrX 130080000 END=134350000;SVLEN=4270000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample23 chrX 130080000 END=134351000;SVLEN=4271000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample14 chrX 130080000 END=134355000;SVLEN=4275000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample16 chrX 130080000 END=134355000;SVLEN=4275000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.53
Sample12 chrX 130082000 END=134352000;SVLEN=4270000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample25 chrX 130082000 END=134402000;SVLEN=4320000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.51
Sample13 chrX 130091000 END=134351000;SVLEN=4260000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.48
Sample21 chrX 134486000 END=144556000;SVLEN=10070000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.49
Sample12 chrX 134496000 END=144424000;SVLEN=9928000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.49
Sample8 chrX 134511000 END=144501000;SVLEN=9990000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.52
Sample4 chrX 134526000 END=145186000;SVLEN=10660000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample23 chrX 134541000 END=144606000;SVLEN=10065000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.49
Sample24 chrX 134546000 END=145206000;SVLEN=10660000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample17 chrX 134626000 END=144831000;SVLEN=10205000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.5
Sample25 chrX 134762000 END=144537000;SVLEN=9775000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.51
Sample19 chrX 134776000 END=144496000;SVLEN=9720000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample10 chrX 134911000 END=145361000;SVLEN=10450000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.49
Sample16 chrX 134916000 END=145416000;SVLEN=10500000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.52
Sample13 chrX 134951000 END=144511000;SVLEN=9560000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.48
Sample15 chrX 134976000 END=144556000;SVLEN=9580000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample14 chrX 134986000 END=144486000;SVLEN=9500000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample5 chrX 134995000 END=144486000;SVLEN=9491000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.49
Sample8 chrX 143862000 END=150267000;SVLEN=6405000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.53
Sample25 chrX 143957000 END=150057000;SVLEN=6100000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample15 chrX 143972000 END=150007000;SVLEN=6035000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample16 chrX 144207000 END=149499000;SVLEN=5292000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.52
Sample24 chrX 144207000 END=150062000;SVLEN=5855000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.52
Sample4 chrX 144272000 END=149499000;SVLEN=5227000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.52
Sample5 chrX 144297000 END=149499000;SVLEN=5202000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.5
Sample23 chrX 144322000 END=150267000;SVLEN=5945000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample14 chrX 144327000 END=150282000;SVLEN=5955000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample19 chrX 144327000 END=150407000;SVLEN=6080000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample12 chrX 144332000 END=150047000;SVLEN=5715000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.49
Sample13 chrX 144333000 END=150438000;SVLEN=6105000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.49
Sample10 chrX 144357000 END=150157000;SVLEN=5800000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5
Sample21 chrX 144367000 END=149499000;SVLEN=5132000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.5
Sample17 chrX 144382000 END=150277000;SVLEN=5895000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.5
Sample19 chrX 149097000 END=153999000;SVLEN=4902000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.49
Sample12 chrX 149182000 END=153999000;SVLEN=4817000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.49
Sample4 chrX 149232000 END=153999000;SVLEN=4767000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.47
Sample14 chrX 149442000 END=153999000;SVLEN=4557000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.5
Sample8 chrX 149457000 END=153999000;SVLEN=4542000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.49
Sample13 chrX 149472000 END=153999000;SVLEN=4527000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.46
Sample16 chrX 149482000 END=153999000;SVLEN=4517000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.51
Sample25 chrX 149487000 END=153999000;SVLEN=4512000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.48
Sample10 chrX 150001000 END=153999000;SVLEN=3998000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.5
Sample24 chrX 150001000 END=153999000;SVLEN=3998000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.47
Sample15 chrX 150001000 END=153999000;SVLEN=3998000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.49
Sample17 chrX 150001000 END=153999000;SVLEN=3998000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.49
Sample21 chrX 150001000 END=153999000;SVLEN=3998000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.49
Sample23 chrX 150001000 END=153999000;SVLEN=3998000;SVTYPE=DEL;CN=0;SVSUPPORT=FALSE 1/1:0:0:0.49
Sample5 chrX 150001000 END=153999000;SVLEN=3998000;SVTYPE=DEL;CN=1;SVSUPPORT=FALSE 0/1:0:0:0.5Have I misunderstood the use of the --ploidy-chr parameter?
Thank you.
CNV plotting fails
Sorry another one:
spectre::2024-03-22 09:49:04,670::INFO::spectre.analysis.analysis> refining cnv calls
spectre::2024-03-22 09:50:14,900::INFO::spectre.spectreCNV> Calculate CNV metrics
spectre::2024-03-22 09:50:32,350::INFO::spectre.analysis.cnv_metrics> DEL border:1.3674360573923894 DUP border:2.623830318153462
spectre::2024-03-22 09:50:32,350::INFO::spectre.spectreCNV> Merge CNV and LoH candidates
spectre::2024-03-22 09:50:32,350::DEBUG::spectre.classes.loh_candidate> CNV cand: 1
spectre::2024-03-22 09:50:32,350::INFO::spectre.spectreCNV> Final candidates are written to .spc file
spectre::2024-03-22 09:50:34,858::INFO::spectre.spectreCNV> Results are writen to bed file
spectre::2024-03-22 09:50:34,866::INFO::spectre.spectreCNV> Results are writen to VCF file
spectre::2024-03-22 09:50:34,877::INFO::spectre.spectreCNV> Result plot in progress
Qt: Session management error: Authentication Rejected, reason : None of the authentication protocols specified are supported and host-based authentication failed
spectre::2024-03-22 09:50:39,004::INFO::spectre.plots.plot> CNVs in chromosome: chr1
Traceback (most recent call last):
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/bin/spectre", line 8, in <module>
sys.exit(main())
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/spectre/spectre.py", line 612, in main
spectre_run.spectre_exe()
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/spectre/spectre.py", line 345, in spectre_exe
spectre_main.cnv_call()
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/spectre/spectreCNV.py", line 130, in cnv_call
self.cnv_analysis.cnv_plot()
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/spectre/analysis/analysis.py", line 730, in cnv_plot
new_plot_device.plot_coverage_cnv(each_chromosome, cov_stats,
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/spectre/plots/plot.py", line 84, in plot_coverage_cnv
self.figure.savefig(f'{self.output_directory}/debug/{self.file_prefix}_plot_cnv_{current_chromosome}.png', dpi=300)
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/matplotlib/figure.py", line 3343, in savefig
self.canvas.print_figure(fname, **kwargs)
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/matplotlib/backends/backend_qtagg.py", line 75, in print_figure
super().print_figure(*args, **kwargs)
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/matplotlib/backend_bases.py", line 2366, in print_figure
result = print_method(
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/matplotlib/backend_bases.py", line 2232, in <lambda>
print_method = functools.wraps(meth)(lambda *args, **kwargs: meth(
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/matplotlib/backends/backend_agg.py", line 509, in print_png
self._print_pil(filename_or_obj, "png", pil_kwargs, metadata)
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/matplotlib/backends/backend_agg.py", line 458, in _print_pil
mpl.image.imsave(
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/matplotlib/image.py", line 1689, in imsave
image.save(fname, **pil_kwargs)
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/PIL/Image.py", line 2410, in save
fp = builtins.open(filename, "w+b")
FileNotFoundError: [Errno 2] No such file or directory: '/rds/projects/b/beggsa-clinicalnanopore/to_share_via_globus/HannahTRun3/D23-51677/20231117_1123_3G_PAS84343_a3d83de8/spectre2/debug/D23-51677_plot_cnv_chr1.png'
Not providing a blacklist leads to stack trace
Command line was:
spectre CNVCaller --coverage mos_depth_out/WTSI-OESO_103.regions.bed.gz --sample-id WTSI-OESO_103 --output-dir WTSI-OESO_103-spectre/ --reference /lustre/scratch126/casm/team154pc/mp15/resources/GCA_000001405.15_GRCh38_no_alt_analysis_set/GCA_000001405.15_GRCh38_no_alt_analysis_set.fa --metadata /lustre/scratch126/casm/team154pc/mp15/resources/GCA_000001405.15_GRCh38_no_alt_analysis_set/GCA_000001405.15_GRCh38_no_alt_analysis_set.mdr
Version:
spectre-cnv==0.2.0
Environment:
contourpy==1.2.1
cycler==0.12.1
fonttools==4.51.0
kiwisolver==1.4.5
matplotlib==3.7.1
numpy==1.24.3
packaging==24.0
pandas==2.0.1
pillow==10.3.0
pyparsing==3.1.2
pysam==0.22.0
python-dateutil==2.9.0.post0
pytz==2024.1
scipy==1.10.1
six==1.16.0
spectre-cnv==0.2.0
tzdata==2024.1
Error is:
spectre::2024-04-17 16:41:48,087::INFO::spectre.spectre> Using existing metadata file /lustre/scratch126/casm/team154pc/mp15/resources/GCA_000001405.15_GRCh38_no_alt_analysis_set/GCA_000001405.15_GRCh38_no_alt_analysis_set.mdr
spectre::2024-04-17 16:41:48,093::INFO::spectre.spectreCNV> Spectre calculating for: mos_depth_out/WTSI-OESO_103.regions.bed.gz
spectre::2024-04-17 16:41:48,094::INFO::spectre.spectreCNV> Data normalization and outlier removal (right tail)
spectre::2024-04-17 16:41:48,508::INFO::spectre.analysis.analysis> Determined bin size from Mosdepth coverage: 1000
Traceback (most recent call last):
File "/lustre/scratch126/casm/team154pc/mp15/ont_duplex/tools/spectre-cnv.venv/bin/spectre", line 8, in <module>
sys.exit(main())
^^^^^^
File "/lustre/scratch126/casm/team154pc/mp15/ont_duplex/tools/spectre-cnv.venv/lib/python3.11/site-packages/spectre/spectre.py", line 612, in main
spectre_run.spectre_exe()
File "/lustre/scratch126/casm/team154pc/mp15/ont_duplex/tools/spectre-cnv.venv/lib/python3.11/site-packages/spectre/spectre.py", line 345, in spectre_exe
spectre_main.cnv_call()
File "/lustre/scratch126/casm/team154pc/mp15/ont_duplex/tools/spectre-cnv.venv/lib/python3.11/site-packages/spectre/spectreCNV.py", line 87, in cnv_call
self.cnv_analysis.data_normalization()
File "/lustre/scratch126/casm/team154pc/mp15/ont_duplex/tools/spectre-cnv.venv/lib/python3.11/site-packages/spectre/analysis/analysis.py", line 116, in data_normalization
self.metadata = fm.load_metadata(mdr_file_path=self.metadata_path,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/lustre/scratch126/casm/team154pc/mp15/ont_duplex/tools/spectre-cnv.venv/lib/python3.11/site-packages/spectre/util/metadata/metadataCollector.py", line 144, in load_metadata
blacklist_content = self.extract_blacklisted_regions(blacklist_file_path)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/lustre/scratch126/casm/team154pc/mp15/ont_duplex/tools/spectre-cnv.venv/lib/python3.11/site-packages/spectre/util/metadata/metadataCollector.py", line 198, in extract_blacklisted_regions
path = os.path.abspath(os.path.expanduser(self.metadata_args.black_list))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'black_list'
I worked around this by creating an empty blacklist containing just chrEBV.
Crash on SNV module
First attempt since my last round of queries... running with Clair3 SNVs and get:
Traceback (most recent call last):
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/bin/spectre", line 8, in <module>
sys.exit(main())
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/spectre/spectre.py", line 614, in main
spectre_run.spectre_exe()
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/spectre/spectre.py", line 349, in spectre_exe
spectre_main.cnv_call()
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/spectre/spectreCNV.py", line 70, in cnv_call
self.snv_analysis.snv_copy_number_state()
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/spectre/analysis/snv_analysis.py", line 230, in snv_copy_number_state
self.snv_multimodal_detect()
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/spectre/analysis/snv_analysis.py", line 103, in snv_multimodal_detect
self.het_dump()
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/spectre/analysis/snv_analysis.py", line 131, in het_dump
het_dump_file = gzip.open(f'{self.spectre_args.out_dir}/debug/het_dump.txt.gz', 'wt')
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/gzip.py", line 58, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/gzip.py", line 174, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/rds/projects/b/beggsa-clinicalnanopore/to_share_via_globus/Rare_Disease_Hannah_Titherage_200623/D2325440/20230620_0810_3E_PAO44618_97828260/spectre2a/debug/het_dump.txt.gz'
Feature Request - tumour-normal calling
Hi Fritz
Would be great if Spectre could support Tumour-Normal input!
Thanks
Andrew
Skips all het SNV sites because deepvariant uses Number=A for the VAF format field.
Hello and thank you for releasing this tool.
The code below (which I am assuming is there to filter multi-allelic sites) causes issues when using Deepvariant's VCFs. Deepvariant uses Number=A for the format VAF field which causes pysam to always parse it as a tuple, even if it is not a multi-allelic site.
if type(snv[self.af_tag]) == tuple:
continue
I was able to get spectre to run as expected by manually changing the VCF header to Number=1 for VAF
I wonder if you would be open to figuring out another way to filter multi-allelic sites. Maybe something like
if len(snv_record.alts) > 1:
continue
Thanks
Jake
RemoveN's
Hi all
Have just tried running Remove N's - and has failed
spectre RemoveNs --reference ~/beggsa-clinicalnanopore/genomes/grch38/genome.fa --output-dir . --output-file grch38-spectre-metadata.mdr --save-only
spectre::2024-03-22 09:44:18,068::INFO::spectre.spectre> Spectre input: RemoveNs --reference /rds/homes/b/beggsa/beggsa-clinicalnanopore/genomes/grch38/genome.fa --output-dir . --output-file grch38-spectre-metadata.mdr --save-only
Traceback (most recent call last):
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/bin/spectre", line 8, in <module>
sys.exit(main())
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/spectre/spectre.py", line 614, in main
main_logger.error("Bin size too small") if spectre_args.bin_size < min_bin_size else ""
AttributeError: 'Namespace' object has no attribute 'bin_size'. Did you mean: 'n_size'?
Core dump issue
Hi
Tried to run spectre.py inside the conda environement.. get a Immediate coredump:
(/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre) [beggsa@bb-pg-login02]$ ~/beggsa-clinicalnanopore/software/Spectre/spectre.py -h
Illegal instruction (core dumped)
blacklist question
Hi Fritz,
I was wondering which blacklist (from what source) you have used for this?
Thanks,
Carolin
Question about QUAL, GQ, FILTER and SVSUPPORT
Hello
The results I get from spectre have many CNVs but all of them have a QUAL=".", GQ=0, FILTER=".", and SVSUPPORT=FALSE. Are these just low quality calls? Would a high quality set all of these fields?
Spectre error
Hi team,
I now have it up and running, but getting:
spectre::INFO> CNV-Metrics: DEL border:1.1658436259509548 DUP border:2.893058579172205
spectre::INFO> refining cnv calls
/Spectre/analysis/analysis.py:384: RuntimeWarning: invalid value encountered in scalar subtract
scaf_cov - np.nanmedian(list(_cand.cov) + list(_cand_next.cov))
spectre::INFO> CNV candidates by SNV
spectre::INFO> Parsing VCF to BED file
/Spectre/util/vcf_parser.py:124: SettingWithCopyWarning:
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead
See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
df_snps_chrom["startbin_"] = pd.cut(x=df_snps_chrom.start_, bins=bins, labels=labels,
/Spectre/util/vcf_parser.py:126: SettingWithCopyWarning:
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead
A lot... then it crashes out with:
spectre::INFO> Calculating CNV events based on SNV data
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/opt/conda/envs/spectre-env/lib/python3.10/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/opt/conda/envs/spectre-env/lib/python3.10/multiprocessing/pool.py", line 48, in mapstar
return list(map(*args))
File "/Spectre/spectre.py", line 117, in outside_spectre_worker
worker.cnv_call()
File "/Spectre/spectreCNV.py", line 112, in cnv_call
self.cnv_analysis.call_cnv_af_region()
File "/Spectre/analysis/analysis.py", line 459, in call_cnv_af_region
self.cnv_calls_list = cnv_by_af.af_cnv_call_region(self.cnv_calls_list, self.snv_af_bed)
File "/Spectre/analysis/call_cnv_AF.py", line 82, in af_cnv_call_region
for af_overlap_candidate in tabix_file.fetch(each_chromosome, each_candidate.start, each_candidate.end):
File "pysam/libctabix.pyx", line 507, in pysam.libctabix.TabixFile.fetch
ValueError: could not create iterator for region 'chr1_KI270706v1_random:38001-54000'
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/Spectre/spectre.py", line 500, in <module>
main()
File "/Spectre/spectre.py", line 482, in main
spectre_run.spectre_exe()
File "/Spectre/spectre.py", line 256, in spectre_exe
results = pool.map(outside_spectre_worker, tuple(spectre_instructions))
File "/opt/conda/envs/spectre-env/lib/python3.10/multiprocessing/pool.py", line 367, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/opt/conda/envs/spectre-env/lib/python3.10/multiprocessing/pool.py", line 774, in get
raise self._value
ValueError: could not create iterator for region 'chr1_KI270706v1_random:38001-54000'
Odd behaviour in VCF and BED files - duplicate entries
Hi Fritz,
I have run Spectre in single sample mode on a large cohort of Nanopore germline samples... I get the same output in the BED and VCF every time:
##Spectre_sample=D23_36899
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT D23_36899
chr17 24225000 Spectre.DEL.0NCMBCW4 N <DEL> . . END=25683000;SVLEN=1458000;SVTYPE=DEL;CN=0 GT:HO:GQ 1/1:0.0:60
chr18 19362000 Spectre.DEL.I5UEYID3 N <DEL> . . END=20560000;SVLEN=1198000;SVTYPE=DEL;CN=0 GT:HO:GQ 1/1:0.0:60
chrX 254000 Spectre.DUP.LK59YCGJ N <DUP> . . END=1925000;SVLEN=1671000;SVTYPE=DUP;CN=4 GT:HO:GQ ./.:0.0:60
chr1_KI270709v1_random 2000 Spectre.DUP.DKZE5SK9 N <DUP> . . END=19000;SVLEN=17000;SVTYPE=DUP;CN=75 GT:HO:GQ ./.:0.0:60
They're all being run in separate folders, within separate runs on the HPC so I can't explain this behaviour. When I look at the CN plots in the directory there are obvious chromosomal arm losses that are not being called in the BED file e.g.:
CNLOH determination fails
Another one.. really sorry:
Just seems to bug out at this point without generating anything... works fine without the --snv option
Spectre input: CNVCaller --coverage mosdepth/D23-51677.regions.bed.gz --sample-id D23-51677 --output-dir spectre2/ --reference /rds/homes/b/beggsa/beggsa-clinicalnanopore/genomes/grch38/genome.fa --blacklist grch38_blacklist_spectre.bed --min-cnv-len 1000 --snv clair/merge_output.vcf.gz
spectre::2024-03-22 10:01:46,588::INFO::spectre.spectre> Spectre version: 0.2.0
spectre::2024-03-22 10:01:46,588::INFO::spectre.spectre> Starting spectre
spectre::2024-03-22 10:01:46,588::INFO::spectre.spectre> Evaluate if a new .mdr file needs to be created
spectre::2024-03-22 10:01:46,588::INFO::spectre.spectre> Looking for default metadata.mdr in output directory
spectre::2024-03-22 10:01:46,588::INFO::spectre.spectre> Using existing metadata file
spectre::2024-03-22 10:01:46,613::INFO::spectre.spectreCNV> Spectre calculating for: mosdepth/D23-51677.regions.bed.gz
spectre::2024-03-22 10:01:46,613::INFO::spectre.spectreCNV> Analysing CN neutral state from SNV data
About min_cnv_len
Dear all
Thanks for releasing this nice tool.
Now, I'm going to adjust min_cnv_len.
Is there any problem using Spectre for detection of cnv < 100kb?
Is there limitation of min_cnv_len?
Best
Adaptive sequencing CNV calling
Hi team
I realise that Spectre may struggle on CN calling in adaptive sampling due to stochastic read depth variation - have a sample that has undergone adaptive LR of BRCA. There is a clear DUP on IGV but both sniffles and spectre fail to pick it up:
We're up to date with latest versions (as far as I am aware).
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