Mutation Analysis (MutSig v2.0 and MutSigCV v0.9 merged result)
Skin Cutaneous Melanoma (Metastatic)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
Maintained by Dan DiCara (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Mutation Analysis (MutSig v2.0 and MutSigCV v0.9 merged result). Broad Institute of MIT and Harvard. doi:10.7908/C1FX77X2
- Overview
+ Introduction
- Summary
  • MAF used for this analysis:SKCM-TM.final_analysis_set.maf

  • Significantly mutated genes (q ≤ 0.1): 117

  • Mutations seen in COSMIC: 754

  • Significantly mutated genes in COSMIC territory: 54

  • Significantly mutated genesets: 2

Mutation Preprocessing
  • Read 279 MAFs of type "Broad"

  • Total number of mutations in input MAFs: 258653

  • After removing 392 mutations outside chr1-24: 258261

  • After removing 1763 blacklisted mutations: 256498

  • After removing 3579 noncoding mutations: 252919

  • After collapsing adjacent/redundant mutations: 228629

Mutation Filtering
  • Number of mutations before filtering: 228629

  • After removing 8252 mutations outside gene set: 220377

  • After removing 346 mutations outside category set: 220031

  • After removing 9 "impossible" mutations in

  • gene-patient-category bins of zero coverage: 211424

- Results
+ Breakdown of Mutations by Type
+ Breakdown of Mutation Rates by Category Type
+ Target Coverage for Each Individual
+ Distribution of Mutation Counts, Coverage, and Mutation Rates Across Samples
+ Lego Plots
+ CoMut Plot
+ Significantly Mutated Genes
+ COSMIC analyses
+ Geneset Analyses
+ Methods & Data