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!

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