Closed philipwfowler closed 1 year ago
This was actually an issue with gumpy
caused by the VCF row being split in such a way that the actual call's position didn't match the position of the minor call.
In this case, it was a minor call of a deletion, as well as an actual call of a deletion in a different position: 779116 . CTGCTGGTGTG C,CTGCTGGTGTGTG
. The actual call being 779126_del_tg
, but the minor call being 779117_del_tgctggtgtg
. The VCF evidence was only stored for the position of the actual call.
Added a fix to gumpy
to ensure that VCF evidence is also stored for the positions of every minor call too: https://github.com/oxfordmmm/gumpy/commit/8794bfc541fc63b4472edd47ecdc195db5355e59
This is the only failure case of this type I found in the 4,128 CRyPTIC VCFs I used to test. Get
VCF attached and minor pop file attached
site.10.subj.TD02495757.lab.TD02495757.iso.1.v0.12.4.per_sample.vcf.zip minor_alleles.txt