I am using
bedtools to test whether a set of variant calls produced by a new method is missing any variants from a set of known validated variants.
bedtools intersect -v -a newcalls.vcf -b goldstandard.vcf
It's working as intended for SNV calls, but it occasionally misses indels due to a single base pair discrepancy. It's usually an alignment artifact that doesn't affect the interpretation of the variant.
My first thought was to make a BED file with intervals that extend a few bp beyond each variant call, and comparing this BED file to the known variants. However, I was wondering whether approximate matching is possible with