Mutation Analysis (MutSig v2.0)
Uveal Melanoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
Maintained by David Heiman (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Mutation Analysis (MutSig v2.0). Broad Institute of MIT and Harvard. doi:10.7908/C1WQ039N
- Overview
+ Introduction
- Summary
  • MAF used for this analysis:UVM-TP.final_analysis_set.maf

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

  • Significantly mutated genes (q ≤ 0.1): 6

  • Mutations seen in COSMIC: 44

  • Significantly mutated genes in COSMIC territory: 5

  • Significantly mutated genesets: 32

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

Mutation Preprocessing
  • Read 80 MAFs of type "maf1"

  • Total number of mutations in input MAFs: 2174

  • After removing 10 blacklisted mutations: 2164

  • After removing 100 noncoding mutations: 2064

Mutation Filtering
  • Number of mutations before filtering: 2064

  • After removing 137 mutations outside gene set: 1927

  • After removing 4 mutations outside category set: 1923

- 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