MuSiC (Mutational Significance in Cancer) 0.3 is now available for download featuring numerous fixes and several new features. MuSiC performs a variety of statistical analyses on the somatic (and germline) alterations discovered in any cancer cohort. Improvements in this version include an enhanced significantly mutated gene test which introduces the ability to 1) take into account sample-specific mutation rates and 2) identify significantly mutated non-genic regions of the genome. The clinical correlation module now features a generalized linear model option allowing for the elimination of covariate influences on mutation-phenotype relationships. Support for MAF 2.2 and for Pfam annotation of GRCh37 (hg19) are now standard. Additionally, several MuSiC components have been optimized and parallelized for faster execution.

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The initial release of TIGRA-SV is available for download. TIGRA-SV is a program that conducts targeted local assembly of structural variants (SV) using the iterative graph routing assembly (TIGRA) algorithm (L. Chen, unpublished). It takes input as a list of putative SV calls and a set of bam files that contain reads mapped to a reference genome. For each SV call, it assembles the set of reads that were mapped or partially mapped to the region of interest (ROI) in the corresponding bam files. TIGRA-SV is quite effective at improving the SV prediction accuracy in short reads analysis and can produce accurate breakpoint sequences.

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The latest release of SomaticSniper, The Genome Institute's somatic SNV calling workhorse, adds an alternative statistical model that better accounts for the rarity of somatic events by jointly considering the tumor and normal genotypes. This version also adds native support for the VCF and BED formats as output. The VCF output contains information useful for downstream filtering, e. g., fraction of reads on the forward and reverse strands, average read mapping quality, and average base quality for reads/bases supporting the variant allele and those supporting the reference allele.

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The latest release of BreakDancer, the Genome Institute's structural variation (SV) detector, is now available for download.
The new release has small bug fixes to ensure it runs reliably on the latest Ubuntu distribution. It is now available as a deb package, installable readily onto Ubuntu Linux or other Debian-based systems.

Installation Instructions

The new Genome Modeling Tools web site is now live. In addition to a new look and feel, this site is automatically updated as internal software at The Genome Institute at Washington University School of Medicine develops.

Software available from this site has been automatically tested and packaged for Ubuntu Linux, with complete documentation for the current release, and previous releases.

Computational biologists can use the tools as-is, or fork them on github to customize them, and contribute improvements back to the genomics community.

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