Tool: Varscan: Variant Detection In Massively Parallel Sequencing Data
gravatar for Istvan Albert
7.4 years ago by
Istvan Albert ♦♦ 81k
University Park, USA
Istvan Albert ♦♦ 81k wrote:

VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, IonTorrent, Roche/454, and similar instruments. The newest version, VarScan 2, is written in Java, so it runs on most operating systems. It can be used to detect different types of variation:

  • Germline variants (SNPs an dindels) in individual samples or pools of samples.
  • Shared and private variants in multi-sample datasets (with mpileup).
  • Somatic mutations, LOH events, and germline variants in tumor-normal pairs.
  • Somatic copy number alterations (CNAs) in tumor-normal exome data

VarScan is under continued development and improvement at a leading genome center with early access to new sequencing technologies, substantial computing resources, immense public/private datasets, and established expertise in sequencing, genetics, and genomics


indel varscan tool snp • 2.3k views
ADD COMMENTlink modified 2.1 years ago by AcademicDialysis70 • written 7.4 years ago by Istvan Albert ♦♦ 81k

Does VarScan2 work for somatic mutation calling against pooled normal samples? I see that it works for germline calling against a pool of normals, and somatic calling against matched-normal data. Is there a way I can "hack" either method?


ADD REPLYlink written 2.1 years ago by AcademicDialysis70
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