extracting snps from multiple vcf file but present in proportion of samples

Question

[ankit hinsu]

Hi,

I have vcf files of 25 samples (all of them prepared using freebayes with same reference). I want to extract SNPs which are present in at least 80% of samples (i.e. present in any 20 samples). Kindly help me with it.

I have tried "bcftools isec". It gives me output of those SNPs which are present in at least 20 samples (what I want). But whichever sample was inputted first in file list will be used as a reference. Because of these, only SNPs which are present in my first sample along with any other 19 samples are outputted (This is what I don't want). It should output SNPs present in any 20 samples.

Hope I have explained my problem clearly.

Ankit.

Answer 1

[Pierre Lindenbaum]

using vcffilterjdk : http://lindenb.github.io/jvarkit/VcfFilterJdk.html

java -jar jvarkit-git/dist/vcffilterjdk.jar -e 'return variant.getGenotypes().stream().filter(G->!(G.isNoCall() || G.isHomRef())).count()>=20;' input.vcf

[ankit hinsu]

Thanks for reply...

I am guessing I need to merge all vcf file and then use this...