Filtering large VCFs by allele freqency using bcftools split-vep function

Question

[tacrolimus]

Dear Biostars community,

I have a large VCF file that has been annotated using VEP. The intrinsic filtering function built into VEP whilst effective is very slow across large VCFs from my experience.

I have been playing around with the spli-vep plug-in on bcftools and found it to be much faster, however, I am struggling to get it to work with allele frequency.

The VCF is a standard format v4.1 VCF. I want to pull the alleles out that are <0.01 by MAX_AF. I am running the following script:

bcftools +split-vep vcf_file.vcf -i 'MAX_AF<0.01' -f -A -s worst

when running this I get an error saying 'MAX_AF' not defined in the vcf header but when running

bcftools +split-vep test/split-vep.vcf -l | less

It appears in the list.

Has anyone else used this tool to filter on allele_frequency?

Many thanks

[scchess]

Do you have a solution?

[tacrolimus]

Afraid not no sorry!