I have a large vcf file and I would like to keep only the pass entries in the filter column.
Is there a way to do this with Variant Annotation?
I know that we can subset on the fields
## Subset on 'fixed', 'info' or 'geno' fields: param <- ScanVcfParam(fixed="ALT", geno=c("GT", "HQ"), info=c("NS", "AF")) vcf_tab <- readVcf(tab, "hg19", param)
but can we further select entries within these fields?
Thank you in advance