after running some benchmarks, i found that our score was broken:
old
new
After looking at the truth set and the changes, I think the error is that DEL must have a negative SVLEN.
Also, an INS does not have an SVLEN of 0, but the distance on the Read.
VCF 4.3 Specification:
"The following INFO keys are reserved for encoding structural variants. In general, when these keys are used by
imprecise variants, the values should be best estimates. When a key reflects a property of a single alt allele (e.g.
SVLEN), then when there are multiple alt alleles there will be multiple values for the key corresponding to each
allele (e.g. SVLEN=-100,-110 for a deletion with two distinct alt alleles)."
After looking at the truth set and the changes, I think the error is that DEL must have a negative SVLEN. Also, an INS does not have an SVLEN of 0, but the distance on the Read.
VCF 4.3 Specification: "The following INFO keys are reserved for encoding structural variants. In general, when these keys are used by imprecise variants, the values should be best estimates. When a key reflects a property of a single alt allele (e.g. SVLEN), then when there are multiple alt alleles there will be multiple values for the key corresponding to each allele (e.g. SVLEN=-100,-110 for a deletion with two distinct alt alleles)."