Subset a VCF based on a certain string within VEP/ClinVar annotation

Question

[Vanish007]

Hi all,

I am trying to subset my extremely large vcf file of around 11,000 samples based on the string "pathogenic". I tried the following:

bcftools view -i 'CSQ="Pathogenic"' -o PathOnlyClinVar.vcf Merged.vcf.gz

which I believe should have worked, but it only returned the header without any other information. I mainly want to safely subset my vcf file with ClinVar information that contains the string "Pathogenic".

Thanks!

Answer 1

[Pierre Lindenbaum]

https://samtools.github.io/bcftools/bcftools.html#expressions

regex operators "~" and its negation "!~". The expressions are case sensitive unless "/i" is added.

bcftools view -i 'CSQ ~ "Pathogenic"' -o PathOnlyClinVar.vcf Merged.vcf.gz

[Vanish007]

Thank you, that seemed to do the trick! I'll have to brush up on my regex :)