Pindel

Overview

Pindel is a pattern growth algorithm for detecting break points of large deletions, medium-sized insertions, inversions, tandem duplications, and other structural variants at single-base resolution from paired-end short-read sequencing data. It is particularly sensitive for detecting insertion/deletion events that are difficult to call with standard short-read aligners.

Used by

  • Used in ICGC PedBrain pilocytic astrocytoma WGS study (96 cases, hg19) alongside crest and delly for somatic SV detection; contributed to identifying structural rearrangements including BRAF fusions in the MAPK-pathway-driven pilocytic astrocytoma cohort PMID:23817572
  • Used for small insertion/deletion detection in paired tumor/normal whole-exome sequencing of grade II glioma initial/recurrent pairs (n=23), complementing MuTect for SNV calling PMID:24336570
  • PInDel used for indel detection in the HGSC Mercury pipeline processing whole-exome sequencing data from 160 periampullary tumors; detected ELF3 frameshift/nonsense inactivating mutations PMID:26804919
  • Used for indel detection in the plasmacytoid-variant bladder cancer WES discovery cohort; contributed to identifying CDH1 frameshift truncating mutations. PMID:26901067
  • Used as one of three somatic variant callers in the MSK-IMPACT pipeline (union of MuTect, Pindel, GATK somatic indel detector) for SNV and indel detection across 10,945 tumors PMID:28481359
  • Applied for somatic indel detection in MET500 whole-exome sequencing data (500 metastatic solid tumors, GRCh37/hg19 alignment) as part of the bioinformatics pipeline alongside VarScan2 and ANNOVAR PMID:28783718
  • One of seven callers in the TCGA MC3 pipeline; made the most indel calls overall, but >130K calls clustered in two samples indicating sample-specific artifacts; used Pindel-priority merging for complex indels PMID:29596782

Notes

  • Corpus-grown slug; not found in cBioPortal canonical gene panel ontology.
  • Specialized in detecting events that confound standard alignment-based variant callers, including medium-to-large indels.

Sources

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

This page was processed by wiki-cli on 2026-05-15. - PMID:28783718

This page was processed by wiki-cli on 2026-05-15. - PMID:29596782

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