VEP filtering query

Question

[prasundutta87]

Hi,

I am trying to filter my VEP (v110.1) annotated structural variation VCF file. I have a set of genes and I need only HIGH and MODERATE impact variants overlapping those genes. I am using this command for the same-

filter_vep \
  -i family_and_de_novo_SVs/test_SVs.vcf.gz \
  -o test_panel.vcf \
  --format vcf \
  --force_overwrite \
  --only_matched \
  --filter "SYMBOL in <comma separated gene lists>" and "IMPACT is HIGH or IMPACT is MODERATE"

My question is- is this the correct way to go ahead? I am somehow getting MODIFIERS in my output as well which I am not interested in. I can filter them downstream, but just wondering why filter_vep is keeping them.

Regards,
Prasun

Answer 1

[Ram]

Try:

--filter "(SYMBOL in <comma separated gene lists>) and (IMPACT is HIGH or IMPACT is MODERATE)"

[prasundutta87]

Thanks Ram, just tried. Still getting MODIFIERS in another test case.

[prasundutta87]

Just correcting myself here after I revisited the command- I had missed --only_matched. So, re-running the full command with it did the job. Thanks for the help.

[Ram]

I've moved my post to an answer. Please accept it to provide closure to the question.