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!
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I'm partial to bambino:
hooking up annovar on the back end provides some good annotation. -
The Genome Institute at Washington University in St. Louis makes software available at
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 callerLast edited by m_two; 07-26-2013, 09:44 AM.Comment
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Comparing somatic mutation-callers: beyond Venn diagrams
Su Yeon Kim and Terence P Speed
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Related:
Global optimization of somatic variant identification in cancer genomes with a global community challenge
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