Mutation Analysis (MutSig v2.0)
Kidney Renal Papillary Cell Carcinoma (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/C1F47NJ5
- Overview
+ Introduction
- Summary
  • MAF used for this analysis:KIRP-TP.final_analysis_set.maf

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

  • Significantly mutated genes (q ≤ 0.1): 30

  • Mutations seen in COSMIC: 82

  • Significantly mutated genes in COSMIC territory: 11

  • Significantly mutated genesets: 1

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

Mutation Preprocessing
  • Read 282 MAFs of type "maf1"

  • Total number of mutations in input MAFs: 18668

  • After removing 123 mutations outside chr1-24: 18545

  • After removing 146 blacklisted mutations: 18399

  • After removing 388 noncoding mutations: 18011

  • After collapsing adjacent/redundant mutations: 17948

Mutation Filtering
  • Number of mutations before filtering: 17948

  • After removing 984 mutations outside gene set: 16964

  • After removing 64 mutations outside category set: 16900

  • After removing 9 "impossible" mutations in

  • gene-patient-category bins of zero coverage: 15843

- 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