Indelocator

Overview

Indelocator is a somatic indel (insertion/deletion) caller developed at the Broad Institute. It detects small insertions and deletions in tumor/normal paired sequencing data by comparing read alignments and applying statistical filters to identify somatic events. Indelocator is commonly run in tandem with MuTect (which handles SNVs) to provide a complete somatic small-variant callset for cancer genome studies.

Used by

  • Applied alongside MuTect, dRanger, BreakPointer, CLONET, ChainFinder, ABSOLUTE, and GISTIC v2 in WGS analysis of 57 prostate tumors; total cohort had 356,136 somatic base-pair mutations with an average of 33 non-silent exonic mutations per primary tumor PMID:23622249
  • Used for indel calling in 149 esophageal adenocarcinoma WGS/WES pairs alongside MuTect; median 104 non-silent coding mutations per tumor PMID:23525077
  • Used to call somatic indels from whole-exome data of 45 BRAF V600 metastatic melanoma FFPE tumors (DeCOG cohort) as part of the Broad Picard/Firehose pipeline alongside MuTect for SNVs PMID:24265153.
  • Used to call somatic indels in 50 muscle-invasive urothelial carcinoma tumors as part of the cisplatin-response WES study. PMID:25096233
  • One of four mutation callers (MuTect, Indelocator, VarScan, RADIA) used in ≥2-caller consensus strategy for somatic indel detection in 820 TCGA diffuse glioma exomes PMID:26824661
  • Used alongside Strelka for indel calling in 619 CRC FFPE tumor/normal WES pairs; concordant calls from both tools were retained to reduce false positives PMID:27149842
  • Used alongside MuTect for indel calling in 1,144 NSCLC (660 lung ADC + 484 lung SqCC) tumor/normal exome pairs PMID:27158780
  • Applied alongside MuTect for indel calling in 412 BLCA whole-exome sequencing tumor-normal pairs PMID:28988769
  • One of seven callers in the TCGA MC3 pipeline; run by Broad Firehose alongside MuTect and ContEst PMID:29596782

Notes

  • Designed for paired tumor/normal analysis; not intended for tumor-only calling.
  • Typically used in conjunction with MuTect for comprehensive somatic SNV+indel discovery.
  • Outputs feed into significance callers (e.g., MutSig) and manual validation workflows.

Sources

This page was processed by crosslinker on 2026-05-09. - PMID:24265153

This page was processed by crosslinker on 2026-05-09. - PMID:25096233

This page was processed by wiki-cli on 2026-05-11. - PMID:26824661

This page was processed by wiki-cli on 2026-05-14. - PMID:27149842

This page was processed by wiki-cli on 2026-05-14. - PMID:27158780

This page was processed by wiki-cli on 2026-05-14. - PMID:28988769

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This page was processed by wiki-cli on 2026-05-15.