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".