Mutation Significance (MutSig) #

It’s a software to analysis the significant mutation from the given mutations from the coherts of the cancer samples. Mainly it’s designed to predict the significance of somatic mutations, it can also be used for germline mutations studies. It will provide background mutation rate (probability of the background mutations), p-value and FDR values or each genes, which given as a Inputs. Also used to cluster the mutations based on hotspots and conservation of the mutation sites. Total its used to access four kind of signals 1. Abundance, 2. Clusters, 3. Conservation and Covariates. All this four signals were updated one by one from the initial version to recent one. Currently it known as MutSigCV.

Input #

mutations.maf (mutation table)

coverage.txt (coverage table)

covariates.txt (covariates table)

Output files #

There are 5 files that MutSigCV outputs:

1) Var_results.categs.txt

2) Var_results.coverage.txt

3) Var_results.mutations.txt

4) Var_results.mutcateg_discovery.txt

5) Var_results.sig_genes.txt

Command #

run_MutSigCV.sh mutations.maf coverage.txt covariates.txt output.txt

Reference #

1) Lawrence, M. et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 499, 214-218 (2013).

2) http://www.broadinstitute.org/cancer/cga/mutsig

3) http://www.broadinstitute.org/cancer/cga/mutsig_run