Hello,
I have about 150 bacterial whole genome sequences that I would like to use to create a multi-sample VCF for downstream analysis. I am using BWA to map to the reference genome and then use Pilon to do the variant calling to produce individual VCF files. I am then merging the individual files using bcf tools merge to create a multi-sample VCF. The problem is that positions there are a large number of no calls in the multi-sample vcf because not every strain has a call at every position.
Any suggestions for a better way to create the multi-sample VCF? Thanks in advance!
Michael
2 answers
I think GATK CombineVariants could help you out here.
You can try to do joint variant calling from multiple samples at once. This can be more robust than individually calling variants on each sample. Not sure if pilon supports that, it looks like it addresses some more complicated variants like structural and assembly issue related things.
Some links
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Splitting VCF/BCF file into seperate gene files
written by Lynne-95 •
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Forum: Best practices for merging vcfs with different positions + different samples?
written by pabe •
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Building vcf from most common alleles
written by Eugene •
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Criteria for merging multiple VCF files
written by seta
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How to get VCF file into a data matrix form for machine-learning? (new to vcf files)
written by jespinoz •
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Do freeBayes and platypus support gVCF (ie incremental variant calling for large sets of genomes)
written by William
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split 1000genomes .vcf per individual
written by User6891
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Multi-Sample Vcf To Phylogenetic Tree.
written by William
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Combine Single Sample Vcf To Multi Sample Vcf
written by William
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What Is The Expected Size Of A Whole Genome Vcf And Bcf?
written by Jeremy Leipzig
Hi Michael,
You might not know markdown, but adding a tab/four spaces before a text block creates "code" layout, which was rather annoying for your post. Fixed that!
Cheers, Wouter