SNV report is not consistent with the bam file

Question

SNV report is not consistent with the bam file

HJTsai opened this issue 5 years ago · comments

HJTsai commented 5 years ago

Hi,

These figures show a INDEL was reported, however there are no INDEL in the bam file.

Could you help us to resolve this problem?

Thanks

HJ Tsai

Ruibang Luo · Answer 1 · Mon Sep 02 2019 22:55:37 GMT+0800 (China Standard Time)

It's possible that even without read support, the network thinks a variant should exist, the AF will be 0 for these cases. You might want to remove all the calls with 0 AF before using them for analysis.

Please also try Clair, which is a newer version of Clariovyante, https://github.com/HKU-BAL/Clair.