Mutation Analysis (MutSig v1.5)
Skin Cutaneous Melanoma (Metastatic)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
Maintained by David Heiman (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Mutation Analysis (MutSig v1.5). Broad Institute of MIT and Harvard. doi:10.7908/C1RR1XCZ
- Overview
+ Introduction
- Summary
  • MAF used for this analysis:SKCM-TM.final_analysis_set.maf

  • Blacklist used for this analysis: pancan_mutation_blacklist.v14.hg19.txt

  • Significantly mutated genes (q ≤ 0.1): 63

  • Mutations seen in COSMIC: 797

  • Significantly mutated genes in COSMIC territory: 58

  • Significantly mutated genesets: 2

  • Significantly mutated genesets: (excluding sig. mutated genes):0

Mutation Preprocessing
  • Read 290 MAFs of type "Broad"

  • Total number of mutations in input MAFs: 276749

  • After removing 22 mutations outside chr1-24: 276727

  • After removing 1815 blacklisted mutations: 274912

  • After removing 9302 noncoding mutations: 265610

  • After collapsing adjacent/redundant mutations: 240711

Mutation Filtering
  • Number of mutations before filtering: 240711

  • After removing 11114 mutations outside gene set: 229597

  • After removing 615 mutations outside category set: 228982

  • After removing 8 "impossible" mutations in

  • gene-patient-category bins of zero coverage: 217245

- 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