Alternative to GATK's VariantFiltration

[finswimmer]

Hello,

as I'm working in a business company I'm not allowed to use GATK without a expensive license. So I'm looking for an alternative for GATK's VariantFiltration module.

What I'm searching is a simply way to add values to the FILTER field due to values (or calculated values) from the INFO and FORMAT annotations.

Thanks for any advice.

fin swimmer

[finswimmer]

SnpEff seems to do what I wanted.

It seems that I cannot add more than one filter at time and have to run it for every filter again on the newly created vcf file. But that's ok for now.

I'm happy to hear about other solutions.

fin swimmer

[vivek_]

If hard filtering is what you want to do, you can simply write scripts to parse the VCF and either modify the QUAL column in the VCF or simply exclude variants.

However the GATK's variant filtering recommendation is VQSR which uses machine learning to classify variants using known sets. I've not come across something similar from any other tool kit.

[finswimmer]

Of course it's not that hard to parse a vcf file. But if there is something commonly used out there, it's much less error prone.

VQSR is nothing I can use here, because I'm doing targeted resequencing and not whole-genome or exom sequencing. So not enough data.

fin swimmer

[finswimmer]

bcftools is doing this job also very nice, with the benefit I can use pipes. So intermediate files arent't needed.