We've moved!
This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!

DP different in IGV and GVCF file

Hello everyone,

I have aligned my exome sample using Dragen Germline Application on Basespace which resulted in corresponding GVCF and .bam files. I was interested in a particular variant on chr11, when I see this variant in the GVCF file I see that DP is 89 where as when I load the .bam file in IGV I see only 68 reads. I have also tried removing the filters (duplicate and vendor failed) in IGV and I am still getting depth as 72. Can you please explain me as to why these are getting filtered.

Answers

Sign In or Register to comment.