Comments (4)
Hi,
I'd like to follow up on this question, is there a liftovered version of the human ancestor file available? Or can we just use the same fasta file?
Thanks
M
from loftee.
Hi can you please share whatever command you have been using for Loftee annotation ? I am using below command and not getting even one LOF Mutation in my VCF files.
perl /gpfs/software/genomics/VEP/ensembl-tools-release-83/scripts/variant_effect_predictor/variant_effect_predictor.pl -i PMC01_jointCalling.filtered.snps.indels.vcf --cache --assembly GRCh37 --offline --dir_cache /gpfs/projects/vep/ --vcf --everything --sift --polyphen --hgvs --fasta /gpfs/projects/refData/Homo_sapiens.GRCh37.dna.primary_assembly.fa --force --symbol --dir_plugins /gpfs/software/genomics/VEP/loftee -o PMC01_jointCalling.filtered.snps.indels_VEP.vcf
perl /gpfs/software/genomics/VEP/ensembl-tools-release-83/scripts/variant_effect_predictor/variant_effect_predictor.pl -i PMC01_jointCalling.filtered.snps.indels.vcf --cache --assembly GRCh37 --offline --dir_cache /gpfs/projects/vep/ --vcf --everything --sift --polyphen --hgvs --fasta /gpfs/projects/refData/Homo_sapiens.GRCh37.dna.primary_assembly.fa --force --symbol --dir_plugins /gpfs/software/genomics/VEP/loftee ----plugin LoF -o PMC01_jointCalling.filtered.snps.indels_VEP.vcf
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@matthdsm did you find a resolution to this issue?
from loftee.
Hi @rvernica
Not exactly, I've just started using the reference genome.
Cheers
M
from loftee.
Related Issues (20)
- Ancestor files no longer available? HOT 1
- [faidx] Zero length sequence:
- MSG: Slice start cannot be greater than slice end
- vep plugin doesnt tag lof variants HOT 1
- doesn't annotate certain LoF suspected variants?
- Loss of END_TRUNC in GRCh38 vs GRCh37 due to change in GERP cutoff from +180 to -58 HOT 1
- WARNING: Plugin 'LoF' went wrong: Undefined subroutine &LoF::reverse_complement called at $CONDA_PREFIX/share/ensembl-vep-111.0-0/LoF.pm line 491
- WARNING: Failed to compile plugin LoF: Can't locate Bio/DB/BigWig.pm in @INC (you may need to install the Bio::DB::BigWig module)
- LOFTEE for CHM13
- GRCh38 branch does not work with GRCh37 data
- No splice site and ancestral allele annotations
- Need to mention in README that master branch has issues with GRCh38 HOT 2
- SQL Database not accessible HOT 1
- Error: lib/Bio/DB/BigFile.c: loadable library and perl binaries are mismatched (got handshake key 0xed00080, needed 0xeb00080)
- Loftee VEP plugin creates incorrectly formatted VCFs
- WARNING: Plugin 'LoF' went wrong: Can't locate object method "prepare" via package "false" (perhaps you forgot to load "false"?) HOT 3
- GERP bigwig file location not concatenated properly HOT 4
- Suggested GERP bigwig download path is very slow and possibly out-of-date HOT 1
- In --tab output format, "PHYLOCSF_TOO_SHORT" shows up in the LoF_info column instead of the LoF_flags column
- Can't exec "samtools" HOT 1
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