Entering edit mode
8.4 years ago
jona
▴
10
Hi all
I am working on a pipeline for SNP calling using muTect. I find many mentions in online forums that the GATK tools for variant calling take account of the quality scores, and they advise against doing any quality trimming in the head of that pipeline.
Does anybody have any experience with muTect, and how it performs with and without trimming low quality reads?
Thanks!
which data are you calling your variants from? exome-seq/WGS/RNASeq?