Tool: Varscan: Variant Detection In Massively Parallel Sequencing Data
3
gravatar for Istvan Albert
6.9 years ago by
Istvan Albert ♦♦ 79k
University Park, USA
Istvan Albert ♦♦ 79k 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

See: http://varscan.sourceforge.net/

indel varscan tool snp • 2.2k views
ADD COMMENTlink modified 19 months ago by AcademicDialysis60 • written 6.9 years ago by Istvan Albert ♦♦ 79k

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?

Thanks!

ADD REPLYlink written 19 months ago by AcademicDialysis60
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1039 users visited in the last hour