About the case-control analysis in Illumina Short-read WGS Data about xtea HOT 3 CLOSED

It looks like there are allele dropouts in the case. See the two heterozygous snps on the right of the screenshot.

from xtea.

Thanks for the reply.

Based on our findings, the allele frequency in the tumor (case) and matched normal (control) samples was determined to be 0.545. How should we interpret an allele frequency of 0.545 in the context of potential allele dropout? Specifically, can we conclude that despite possible allele dropout in the tumor sample, there is an insertion in the region? Or should this insertion in the tumor sample only be considered a sequencing artifact?

from xtea.

It's a germline insertion. That's why you observed it in both the case and control. I mean in the tumor sample, there is an allele dropout, thus the VAF is lower than in the control.

from xtea.