SnpSift annotate seems to be including a variant allele that is not in my input VCF, when I annotate to clinVar.
For example, here's a row from a test VCF:
1 201364336 rs74315379 G A
G>A is the only call made. G matches the reference assembly.
Yet in the INFO field, we get:
Why would SnpSift be also reporting the G>T variant? There is only 1 data row in the test file and no mixed allele frequencies or anything else to confound the annotation. It should just be reporting records matching the A variant allele because other alleles are not present in my sample.
Sure hope I'm missing something obvious here, but it appears to be grabbing every possible variant for that position from the VCF I'm annotating to (just those two exist for that position in ClinVar), without regard to the actual variant allele. Is there any way to make SnpSift do what I want here and just annotate to the variant that's in my sample?
(Edits for clarity)