Mutect2

Description

Mutect2 is a variant caller that calls somatic SNVs and indels via local assembly of haplotypes. It is included into Genome Analysis Toolkit a collection of command-line tools for analyzing high-throughput sequencing data with a primary focus on variant discovery.

It can be used with two modes:

1. tumor-normal mode where a tumor sample is matched with a normal sample in analysis.
2. tumor-only mode where a single sample's alignment data undergoes analysis

Requirements

To run Mutect2, the program required the following files:

-Tumor bam file. -Normal bam file. (Only required in the tumor-normal mode) -reference file in fasta format.

Mutect2 does not require a germline resource nor a panel of normals (PoN) to run, although both are recommended. -germline resource: -panel of normals vcf file. To create a PoN, call on each normal sample in this mode, then use CreateSomaticPanelOfNormals to generate the PoN.

Usage

(i) Tumor with matched normal

     gatk Mutect2 \
     -R reference.fa \
     -I tumor.bam \
     -I normal.bam \
     -normal normal_sample_name \
     --germline-resource af-only-gnomad.vcf.gz \
     --panel-of-normals pon.vcf.gz \
     -O somatic.vcf.gz

(ii) Tumor-only mode

    gatk Mutect2 \
    -R reference.fa \
    -I sample.bam \
    --germline-resource af-only-gnomad.vcf.gz \
    --panel-of-normals pon.vcf.gz \
    -O single_sample.vcf.gz

Best Practises

Mutect2 can be also used together with other GATK tools for complete workflows. Check for Best Practices Workflows

Somatic short variant discovery workflow includes the following steps:

• Call candidate variants: Mutect2
• Calculate Contamination:
• Learn Orientation Bias Artifacts
• Filter Variants

Reference

• Mutect2 official webpage
• Joan Enric