Next generation sequencing

Post-analysis categorization
- Literature search
Post-survey categorization
- Features validated in most cases
- Features not validated
Simple lists
Preliminary lists

Tool name

VarScan

URL

http://varscan.sourceforge.net/

Important features

1. VarScan is able to detect SNPs and indels from both Solexa and Roche platforms. 2. Unlike currently available variant detection tools, VarScan is compatible with several read aligners (BLAT, Newbler, cross_match, Bowtie and Novoalign) and calls variants in both individual and pooled samples. 3. As an input VarScan requires an alignment file. As an output, user gets reports of SNPs, insertions and deletions with their chromosomal coordinates, alleles, flanking sequence and read counts.

Citations

Koboldt DC, Chen K, Wylie T, Larson DE, McLellan MD, Mardis ER, Weinstock GM, Wilson RK, Ding L. VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics. 2009 Sep 1;25(17):2283-5. Epub 2009 Jun 19. PMID: 19542151

Year of publication

2009

Rank by usage frequency

100

Comments

Function

SNP discovery, Indel discovery