Filter genotype in multi-sample VCF file

Question

[guillaume.rbt]

Hello,

I've done a multi-sample SNP calling with samtools mpileup, and my results are in a vcf file.

I would like to keep only SNPs detected on all of my samples (without any sample with GT flag = 0/0 ,(homozygote for the reference allele)).

Does anyone know a tool that could do it?

Thanks!

[Rm]

vcffilter -g "! (GT = 0/0 )"  Input.vcf

[Ram]

Um, What's the vcffilter binary a part of?

EDIT: NVM, I found it on GitHub. vcflib

Answer 1

[Jorge Amigo]

I usually choose vcftools or bcftools to deal with vcf files, but in your case a simple grep would do:

grep -v "0[/|]0" <in.vcf >out.vcf

[guillaume.rbt]

indeed, a grep works just fine, good idea! thank you all

[Jorge Amigo]

usually vcf files require vcf software, although sometimes you just have to (carefully) go for the simplest solution, and simple bash one-liners may be of great help. in this particular case, grep should even be faster than any other proper-vcf-handling software.

[Ram]

I agree with the approach, but it would be prudent to watch out for false matches. We are, after all, just matching string expressions and not ensuring that the 0[/|]0 matches the genotype data specifically.

[Jorge Amigo]

in a properly formatted vcf file, the "0[/|]0" pattern will only match reference homozigotes in columns 10 and on. there's no way that pattern can appear in the headers nor in the previous 1-9 columns, so that's why grep -v "0[/|]0" is so convenient if you want to extract all the variant sites where all samples do vary, because it not only filters exactly what you don't want, but it also outputs a properly formatted vcf file too. if you want to be more strict, you could use a little more complex pattern such as "0[/|]0:" if you are sure that the genotypes' format is always "GT:" plus something else, which could not be always the case. only the GT field is mandatory in the vcf format.

Answer 2

[Ram]

vcftools should help you out.

Here's the genotype filtering options on vcftools

[GouthamAtla]

Is there any way to keep snps that are present at least in n number of samples ?

Answer 3

[iraun]

If you are not very familiar with programming (this problem can be solved with awk/perl scripting), I suggest you SnpSift tool. In my opinion it is an user friendly tool, very intuitive, and with a great examples in the web page that can guide you. You can filter VCF files according to your needs.