quality trimming before muTect?

Question

[jona]

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!

[TriS]

which data are you calling your variants from? exome-seq/WGS/RNASeq?

Answer 1

[jona]

So actually it says so on the mutect webpage here

In brief, muTect consists of three steps.

1. Preprocessing the aligned reads in the tumor and normal sequencing data. In this step we ignore reads with too many mismatches or very low quality scores since these represent noisy reads that introduce more noise than signal.