brwnj / covviz

Multi-sample genome coverage viewer to observe large, coverage-based anomalies alongside annotations and sample metadata

Solving complex issues with Nextflow, Javascript, Python, and anything else necessary to interpret and communicate.

covviz's Issues

Gene ID dropdown not showing options with gff option

Hi Joe,
I am using covviz for ~1500 samples, after generating bed file with golfer indexcov, I am running covviz by following command.

_covviz --ped testcoviz/testcoviz-indexcov.ped --gff ~/scratch/Homo_sapiens.GRCh38.99.gtf.gz testcoviz/testcoviz-indexcov.bed.gz -o CHIP_Coverage

In my html output I don't know see options in GeneID dropdown. Do I have to specify the gene feature ? in option?

referring to this line on documentation "Currently we support GFF, VCF, and BED. GFF tracks are added using --gff where features are 'gene' and attributes have 'Name='. Feature type and attribute regex can be configured using --gff-feature and --gff-attr."

add lines at y=0.5 and y=1.5

this helps to understand if we're seeing what looks to be a heterozygous deletion or duplication.

utilize location.hash for selected chrom and xaxis.range

Error on build_report

Howdy,

I tried to test covviz and ran into errors when building the final report - It reported that there were no traces on any of the chromosomes (see below) but I did check NF-indexcov.bed.gz and there were indeed values for each of the samples in a standard looking bed3+.
I'm not sure what else could be wrong, do you have any advice?

Many thanks,

covviz --min-samples 8 --sex-chroms X,Y --exclude '^GL|^hs|EBV$|M$|MT$|^NC|_random$|Un_|^HLA\-|_alt$|hap\d+$'         --z-threshold 3.5 --distance-threshold 150000         --slop 500000 --ped NF-indexcov.ped  --skip-norm NF-indexcov.bed.gz

Command exit status:
1

Command output:
(empty)

Command error:
[INFO] parsing bed file (NF-indexcov.bed.gz)
[INFO] plotting 2 traces on chrom chr1
[INFO] plotting 2 traces on chrom chr10
[INFO] plotting 2 traces on chrom chr11

support multiple annotation tracks

--gff could be nargs='append' and could add others like --bed.

Proportions covered is empty

Hi,

I am using covviz to visualize the coverage across multiple samples.

However, the html file that I obtained does not have anything for the Proportions Covered tab.

This is the command that I used to run covviz

covviz indexcov.bed --ped samplechr.ped --sample-col sample_id --sex-col sex --output 100samples.html

I am running covviz using singularity.

Am I supposed to pass in the .roc file?

Thank you very much.

Hope to hear from you soon.

Best regards,
Joanna

keep sample selected when switching chromosomes

miscellaneous

in getting this to run on non-indexcov output I found a few issues:

1. it requires the .roc output from indexcov which is pretty specific. this can be calculated directly from the bed files.
2. it requires the .ped output from indexcov. this should be optional. and many values can be
3. it requires a gff which defaults to $gff. all of the parameters are defaulting to the string literal $gff or $roc. this makes it odd to call from the command-line. for example it looks for $sex_ chroms so it's very hard to call from the command-line.
4. there is no information on a sensible value for --z-threshold or --distance or --slop. I don't know what the latter 2 of those are for.
5. all instances in the javascript of $(...) are left escaped as \$(...).

I will work on some of these, but I wanted to document them here.

Unable to find image 'brwnj/covviz:v1.3.2' locally

I'm getting an error when trying to run covviz with nextflow. I'm new to docker/nextflow and was hoping that someone would be able to identify the problem as I followed all the instructions on the covviz page. thanks - Robert

./nextflow run brwnj/covviz -profile docker --exclude --sex --indexes '/media/robert/External_Drive/BAMS/*.bai' --fai /home/robert/assembly/GCF_014851395.1_ASM1485139v1_genomic.fa.fai
N E X T F L O W ~ version 21.04.2
Launching brwnj/covviz [focused_wilson] - revision: 614537d [master]

====================================================================
covviz - find large, coverage-based variations on chromosomes

Homepage / Documentation

https://github.com/brwnj/covviz

Authors

Joe Brown [email protected]

====================================================================

Alignment indexes --indexes : /media/robert/External_Drive/BAMS/*.bai
Reference index --fai : /home/robert/assembly/GCF_014851395.1_ASM1485139v1_genomic.fa.fai
Sex chromosomes --sexchroms : X,Y
Excluded chroms --exclude : true
Z threshold --zthreshold : 3.5
Distance threshold --distancethreshold: 150000
Significant region slop --slop : 500000

====================================================================

executor > local (1)
[b1/5a449d] process > run_indexcov [ 0%] 0 of 1
executor > local (1)
[b1/5a449d] process > run_indexcov [100%] 1 of 1, failed: 1 ✘
[- ] process > merge_peds -
[- ] process > build_report -
Error executing process > 'run_indexcov'

Caused by:
Process run_indexcov terminated with an error exit status (125)

Command executed:

goleft indexcov --sex X,Y --excludepatt "true" --directory NF --fai GCF_014851395.1_ASM1485139v1_genomic.fa.fai RHF05438.bam.bai RHF05338.bam.bai RHF05342.bam.bai RHF05347.bam.bai RHF05358.bam.bai RHF05397.bam.bai RHF05432.bam.bai RHF05301.bam.bai G0620_M02.bam.bai RHF05302.bam.bai RHF05350.bam.bai G0319-20-B0074.bam.bai G0319-20-B0115.bam.bai G0319-20-B0117.bam.bai G0520-1-G359.bam.bai RHF05357.bam.bai RHF05398.bam.bai RHF05440.bam.bai RHF05444.bam.bai RHF05462.bam.bai RHF05464.bam.bai RHF05453.bam.bai RHF05431.bam.bai RHF05421.bam.bai RHF05452.bam.bai
mv NF/* .

Command exit status:
125

Command output:
(empty)

Command error:
Unable to find image 'brwnj/covviz:v1.3.2' locally
docker: Error response from daemon: manifest for brwnj/covviz:v1.3.2 not found: manifest unknown: manifest unknown.
See 'docker run --help'.

Work dir:
/home/robert/tools/work/b1/5a449d420115e8ca3bd6be1f35bae0

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh

add download button to table