Remove not polymorphic sites from VCF

Question

[GabrielMontenegro]

I have a VCF file and I want to remove sites that are not polymorphic sites i.e. sites where all individuals are REF/REF or ALT/ALT. Is there a quick way to do this using bcftools or vcftools?

Thanks.

Answer 1

[finswimmer]

Now I hopefully understand your goal. This will remove side where all samples are either hom ref or hom alt:

$ bcftools view -e 'COUNT(GT="AA")=N_SAMPLES || COUNT(GT="RR")=N_SAMPLES' input.vcf

Have a look at the manual to explore more ways to filter vcf files using bcftools.

I've deleted my old answer, because it hasn't answer your question.

[GabrielMontenegro]

Thanks! Yes, I think that answers my question. I got this error message though: the tag "INFO/COUNT" is not defined in the VCF header. Do you know how to add this info on my vcf?

[finswimmer]

I think you're using an outdated version of bcftools. The method COUNT was introduced in v1.7. The current version is v1.9.

Which version are you using? Please upgrade.

[GabrielMontenegro]

Using v1.9 solved it - Thanks!

[GabrielMontenegro]

@finswimmer have a quick question, will bcftools get the COUNT of the AA or RR genotypes based on the INFO field? Or will it compute the COUNT for all sites? I am applied this filter after merging my dataset with another dataset and I think I am getting weird results.

[finswimmer]

For each line in the vcf file bcftools will have a look at the genotype of each sample. In the INFO column there is no information about the counts.

Why do you think you are getting a weird result? As always, a small example dataset which shows your problem would be helpful.

[Denis]

The command will not work if there are missing genotypes in the given position.

Answer 2

[amy.roberts]

You can also use the -c function in view

-c, --min-ac INT[:nref|:alt1|:minor|:major|:'nonmajor']
minimum allele count (INFO/AC) of sites to be printed. Specifying the type of allele is optional and can be set to non-reference (nref, the default), 1st alternate (alt1), the least frequent (minor), the most frequent (major) or sum of all but the most frequent (nonmajor) alleles.

By setting -c 1, you will only keep sites with at least one nonref allele (=polymorphic in your data)

bcftools view -c 1 input.vcf.gz -o output.vcf.gz -Oz

[Denis]

I'm wondering how can i filter out both the monomorphic reference sites and sites which are monomorphic for the alternative allele?

Answer 3

[Pierre Lindenbaum]

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

 java -jar dist/vcffilterjdk.jar -e 'return !(variant.getGenotypes().stream().allMatch(G->G.isHomVar()) || variant.getGenotypes().stream().allMatch(G->G.isHomRef()));' input.vcf