What's the best tools to detect somatic mutations?

[seqfish]

Hi guys, I am quite new in cancer genome. Can anyone give me some suggestions on tools that can detect somatic mutations from a patient's tissue sequencing data? Thanks!

[Richard Finney]

I'm partial to bambino:

https://cgwb.nci.nih.gov/goldenPath/bamview/documentation/index.html

hooking up annovar on the back end provides some good annotation.

[m_two]

The Genome Institute at Washington University in St. Louis makes software available at

http://tvap.genome.wustl.edu/tools/

You can obtain support through biostar using the "music" tag.

Detection Tools

Bassovac
Improved Bayesian inversion somatic caller

BreakDancer
SV caller using paired-end sequence data

CMDS
Recurrent CNV caller using population data

CNVHMM
An HMM-based copy number caller

CopyCat
A read depth based copy number caller

CREST
SV caller using soft-clipped reads

PASSion
Paired-end RNA-Seq splice site detection

Pindel
Indel caller using pattern growth

SomaticSniper
Bayesian somatic SNV caller
(Useful for situations with normal contamination (ie adjacent normal or tissue infiltrating leukemias)

SquareDancer
Split reads for SV discovery

TIGRA_SV
De novo assembly of SV breakpoints

VarScan
Germline and somatic SNV and CNV caller

[m_two]

Comparing somatic mutation-callers: beyond Venn diagrams
Su Yeon Kim and Terence P Speed

http://www.biomedcentral.com/1471-2105/14/189

[m_two]

Related:

Global optimization of somatic variant identification in cancer genomes with a global community challenge

http://www.nature.com/ng/journal/v46/n4/full/ng.2932.html