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GATK - Mutect2

Call somatic SNVs and indels via local assembly of haplotypes

Input data

In data directory, tool searches for the following in this specific path structure,

• Alignment

  • Normal
    • normal.bam
    • if indexes (optional) are not provided, the tool will create them for you.
  • Tumor
    • tumor.bam

• Reference

  • hg38.fa
  • hg38.fa.fai

• Germline

  • af-only.gnomad.hg38.vcf.gz
  • af-only-gnomad.hg38.vcf.gz.tbi

• Panel of Normals

  • 1000g_pon.hg38.vcf.gz
  • 1000g_pon.hg38.vcf.gz.tbi

Output

Folder name reflects which comparison was done.

• normal_tumor
  • .vcf.gz: somatic variants
  • .vcf.gz.stats: somatic variants stats
  • .vcf.gz.tbi: somatic variants index

Source

https://gatk.broadinstitute.org/hc/en-us/articles/360037593851-Mutect2

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