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Questions tagged [mutect2]

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2 votes
1 answer

Creating custom VCF file

I'm stuck on what seems to be a banal problem, but I can't work out where the issue is. I need to create some customised VCF files that specify particular variants of interest. This is a custom VCF I ...
Nereus's user avatar
  • 209
1 vote
1 answer

How to adjust cutoffs in Mutect2

I'm currently performing some initial analyses on targeted Illumina sequencing data generated with DNA from diseased tissue. My hypothesis is that one particular gene might contain somatic mutations ...
Nereus's user avatar
  • 209
0 votes
1 answer

A bash script for running on a bunch of bam files

I have some bam files in this directory /data/Continuum/WES/results/ I want to run GATK mutation calling over bam files I ...
Zizogolu's user avatar
  • 2,160