Best way to create a multi-sample VCF

Question

[Michael]

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

[WouterDeCoster]

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

Answer 1

[WouterDeCoster]

I think GATK CombineVariants could help you out here.

Answer 2

[cmdcolin]

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

http://gatkforums.broadinstitute.org/gatk/discussion/3893/calling-variants-on-cohorts-of-samples-using-the-haplotypecaller-in-gvcf-mode

http://gatkforums.broadinstitute.org/gatk/discussion/3686/why-do-joint-calling-rather-than-single-sample-calling-retired