Question: quality trimming before muTect?
gravatar for jona
4.3 years ago by
jona10 wrote:

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?


snp quality mutect trimming • 1.2k views
ADD COMMENTlink modified 4.2 years ago • written 4.3 years ago by jona10

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

ADD REPLYlink written 4.3 years ago by TriS4.1k
gravatar for jona
4.2 years ago by
jona10 wrote:

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.
ADD COMMENTlink modified 11 weeks ago by RamRS25k • written 4.2 years ago by jona10
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