GATK Somatic Indel Detector

Overview

GATK Somatic Indel Detector is a variant-calling tool from the Genome Analysis Toolkit (GATK) designed to detect somatic insertion and deletion (indel) events in paired tumor/normal sequencing data. It identifies candidate somatic indels by comparing allele frequencies between tumor and matched normal samples, with configurable thresholds for minimum allele fraction and read support.

Used by

  • coad_caseccc_2015 — used alongside mutect and varscan for somatic indel calling in 29 AA CRC discovery exomes (paired tumor/normal); contributed to identification of 20 significantly mutated genes in African American MSS colorectal cancer including EPHA6 and FLCN as AA-specific drivers PMID:25583493
  • GATK Somatic Indel Detector used for indel calling in 10 PCNSL WES cases alongside SomaticSniper SNV calls; variants annotated with snpEFF/PolyPhen-2 via the TREAT workflow. PMID:25991819
  • GATK Somatic Indel Detector used for indel calling in MSK-IMPACT targeted panel sequencing of pancreatic cancer PMID:26278805
  • GATK Somatic Indel Detector used for indel calling in whole-exome and whole-genome sequencing of colorectal cancer PMID:26343386
  • Used alongside MuTect for indel calling in 62 uRCC tumours sequenced on the MSK-IMPACT 230-gene panel with BWA-MEM-aligned reads. PMID:27713405
  • Used as one of three somatic variant callers in the MSK-IMPACT bioinformatics pipeline (union of MuTect, Pindel, GATK somatic indel detector) for SNV/indel detection PMID:28481359
  • GATK SomaticIndelDetector used for indel calling in 15 Korean vulvar SCC paired tumor/normal WES samples (BWA/hg19 pipeline); 21 mutations across 9 genes validated by digital PCR or Sanger sequencing PMID:29422544

Notes

  • Part of the GATK toolkit; intended for use with BWA-aligned BAM files.
  • Typically used in combination with other somatic callers (MuTect for SNVs, VarScan for SNVs/indels) for increased sensitivity.
  • Superseded in later GATK versions (GATK4+) by Mutect2, which handles both SNVs and indels.

Sources

  • PMID:25583493 — Guda et al. 2015, WES of African American MSS CRC

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This page was processed by entity-page-writer on 2026-05-15. - PMID:27713405

This page was processed by entity-page-writer on 2026-05-15. - PMID:28481359

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