If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
how to select a private SNP with GATK from a multisample VCF file
I ran in to the situation now a couple of times that I need to extract a set of private SNPs from a multisample VCF file. For example in a forward genetics knockout screen of a large set of samples.
It is possible with vcf-contrast from vcf-tools:
vcf-contrast +sample1 -sample2 -sample3 -n input.vcf > private sample1.vcf
vcf-contrast -sample1 +sample2 -sample3 -n input.vcf > private sample2.vcf
vcf-contrast -sample1 -sample2 +sample3 -n input.vcf > private sample3.vcf
After this I still would have to filter out the private 0/0 calls and doing this for a large multisample VCF means entering this command for all the combinations which is not really nice.
Surely this must be possible with GATK. Does anyone know how to do this with GATK.
Maybe it is somewhere in the SelectVariants? The --discordance option looked promissing but there is something about that the samples should be the same? Or is it possible to write another variant walker or a JEXL expression?
P.S. By accident I also posted this question in the XHMM, an admin could remove it there.