Soft filtering of SNPs in a list

Question

[beanavarro85]

Hi all!

I am looking for a way to filter a list of SNPs from a VCF file.

I know that, with GATK SelectVariants or VCFtools you can exclude a list of SNPs from your VCF, however what I want is to soft-filter them (add filter info in the FILTER column of the VCF).

Any ideas? Thanks!

[GouthamAtla]

A small PyVCF snippet should help. I am not sure if VariantFilter just adds "filter_name" or also excludes variants.

[beanavarro85]

I believe VariantFiltration adds "filter_name", but I am unsure on how provide a SNP list as a filter expression. I have never used PyVCF, I'll check that out.

Answer 1

[Pierre Lindenbaum]

GATK VariantFiltration https://gatk.broadinstitute.org/hc/en-us/articles/360037434691-VariantFiltration

I refactored the program I wrote for: How to get 1000 Genomes data in bulk?

it now takes a new option --filter . see http://lindenb.github.io/jvarkit/Biostar332826.html

e.g:

java -jar dist/biostar332826.jar --filter "MYFILTERNAME" -r ids.txt sites.vcf.gz 

Answer 2

[finswimmer]

Hello,

bcftools filter with the -s argument is what you are looking for.

bcftools filter -e 'ID=@rsid.txt' -s 'MyFilter' input.vcf

fin swimmer