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Illumina / canvas

Canvas - Copy number variant (CNV) calling from DNA sequencing data
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vcf contains >1 samples, name for a sample of interest must be provided #116

Closed logust79 closed 5 years ago

logust79 commented 5 years ago

This is somewhat related to issue #81, but his / hers crash for a different reason.

My VCF is multi-sample. From what I can see here, there seems to be no option to name a sample of interest. Hence I suggest to rephrase the error message to say something like 'It only accepts a simple-sample VCF.' https://github.com/Illumina/canvas/blob/ef2941aa4d6a2cf7ebf05458bc268c1c699c73db/Src/Canvas/CanvasSNV/SNVReviewer.cs#L94-L105

eroller commented 5 years ago

please use the small pedigree workflow. germline-wgs has been deprecated

logust79 commented 5 years ago

Thank you for your response. After studying the doc, does something like this work?

dotnet /CanvasDIR/Canvas.dll SmallPedigree-WGS 
--bam=sampleA.bam,,sampleA 
--bam=sampleB.bam,,sampleB 
-r /basespace/Projects/canvas/AppResults/canvasdata/Files/kmer.fa 
-g /basespace/Projects/canvas/AppResults/canvasdata/Files/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta 
--sample-b-allele-vcf /basespace/Projects/canvas/AppResults/snvvcf/Files/Pedigree.vcf.gz 
-f /basespace/Projects/canvas/AppResults/canvasdata/Files/filter13.bed 
-o /tmp/gHapMixDemo

By the way, is it possible to add an option of chromosome of interest? Or I have to mask it in the filter bed? Thank you!

eroller commented 5 years ago

I don't believe comma separated list will work. Use white space to delimit the fields Please try:

dotnet /CanvasDIR/Canvas.dll SmallPedigree-WGS 
--bam sampleA.bam other sampleA 
--bam sampleB.bam other sampleB 
-r /basespace/Projects/canvas/AppResults/canvasdata/Files/kmer.fa 
-g /basespace/Projects/canvas/AppResults/canvasdata/Files/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta 
--sample-b-allele-vcf /basespace/Projects/canvas/AppResults/snvvcf/Files/Pedigree.vcf.gz 
-f /basespace/Projects/canvas/AppResults/canvasdata/Files/filter13.bed 
-o /tmp/gHapMixDemo

WGS does not support single chromosome of interest, but you can try modifying the filter bed file to achieve what you want. We have never tried it, so you may encounter a problem.

logust79 commented 5 years ago

Thank you for your help!