Filtering whilst annotating.

[tirohia]

Is there a way to access the vcf calls on a per-record basis as they are being annotated? Specifically, I'm looking for a way to retain only those vcf calls that have been annotated from at least one source. Don't know if this is possible, or if I have to filter out unannotated calls in a later step?

Thanks Ben.

[brentp]

hi, vcfanno will only annotate, not filter. so you'd have to use a downstream tool like bcftools or slivar to do the filtering.