VarScan

Overview

VarScan is a platform-independent variant detection tool for next-generation sequencing data. It uses a heuristic/statistic approach to call somatic mutations (SNVs and indels) and copy-number alterations in paired tumor-normal samples.

Used by

  • Used for somatic variant calling in MPNST WES discovery cohort (15 tumors) PMID:25240281
  • Used alongside MuTect for somatic variant calling in 78 gastric adenocarcinoma WES samples; joint calling identified a high-clonality (HiC) subtype with distinct C>G mutational enrichment (25% vs. 9% in low-clonality; P=0.002) PMID:25583476
  • Used for somatic variant calling in the AA CRC WES pipeline alongside MuTect, contributing to the mutational landscape analysis of 103 African American MSS colorectal cancers PMID:25583493
  • VarScan used for INDEL calling in 109 microdissected PDA WES samples (≥8 reference reads, ≥3 variant reads); indels manually inspected in IGV before inclusion. PMID:25855536
  • VarScan used for somatic variant calling in whole-exome sequencing of adrenocortical carcinoma PMID:26095796
  • Used for indel calling in whole-genome sequencing of 46 matched primary/recurrent medulloblastoma samples alongside Strelka and MutationSeq; supported characterization of massively increased mutational burden (~5-fold) at recurrence PMID:26760213.
  • One of four mutation callers (MuTect, Indelocator, VarScan, RADIA) used in ≥2-caller consensus strategy for somatic variant detection in 820 TCGA diffuse glioma exomes PMID:26824661
  • Used (as VarScan2) together with Sequenza to generate intersected copy-number profiles from anti-PD-1-treated melanoma WES data PMID:26997480
  • VarScan2 v2.3.2 used for somatic SNV calling in MET500 whole-exome sequencing data (500 metastatic solid tumors, mean 180× tumor / 120× normal coverage, aligned to GRCh37/hg19 via Novoalign) PMID:28783718
  • VarScan 2.3.7 applied as one of four somatic callers in intersection-based SNV detection for 68 paired melanoma WES biopsies in the CA209-038 nivolumab trial PMID:29033130
  • One of seven somatic callers in the TCGA MC3 ensemble pipeline run on the DNAnexus cloud across ~10,510 TCGA tumor/normal pairs PMID:29596782

Notes

  • Commonly paired with MuTect and Strelka in multi-caller somatic variant detection pipelines.
  • Corpus-derived slug; not in cBioPortal gene panel ontology.

Sources

This page was processed by crosslinker on 2026-05-14. - PMID:25583476

This page was processed by crosslinker on 2026-05-14. - PMID:25583493

This page was processed by wiki-cli on 2026-05-14. - PMID:25855536

This page was processed by wiki-cli on 2026-05-14. - PMID:26095796

This page was processed by wiki-cli on 2026-05-14. - PMID:26760213

This page was processed by wiki-cli on 2026-05-14. - PMID:26824661

This page was processed by wiki-cli on 2026-05-14. - PMID:26997480

This page was processed by wiki-cli on 2026-05-14. - PMID:28783718

This page was processed by entity-page-writer on 2026-05-15. - PMID:29033130

This page was processed by entity-page-writer on 2026-05-15. - PMID:29596782

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