TCGA mutations Track Settings
 
TCGA somatic mutations by tumor type

Display mode:       Reset to defaults

Haplotype sorting display

Enable Haplotype sorting display
Haplotype sorting order:
using middle variant in viewing window as anchor.
If this mode is selected and genotypes are phased or homozygous, then each genotype is split into two independent haplotypes. These local haplotypes are clustered by similarity around a central variant. Haplotypes are reordered for display using the clustering tree, which is drawn in the left label area. Local haplotype blocks can often be identified using this display.
To anchor the sorting to a particular variant, click on the variant in the genome browser, and then click on the 'Use this variant' button on the next page.
using the order in which samples appear in the underlying VCF file
Haplotype clustering tree leaf shape:
draw branches whose samples are all identical as <
draw branches whose samples are all identical as [
Allele coloring scheme:
reference alleles invisible, alternate alleles in black
reference alleles in blue, alternate alleles in red
first base of allele (A = red, C = blue, G = green, T = magenta)
Haplotype sorting display height:

Filters

Exclude variants with Quality/confidence score (QUAL) score less than
Minimum minor allele frequency (if INFO column includes AF or AC+AN):


Display data as a density graph:

VCF configuration help

All subtracks:
List subtracks: only selected/visible    all    ()  
dense
 Configure 		 Bladder  TCGA Bladder urothelial carcinoma (BLCA)   Data format 
dense
 Configure 		 Brain Lower Grade  TCGA Brain Lower Grade Glioma (LGG)   Data format 
dense
 Configure 		 Breast Invasive  TCGA Breast invasive carcinoma (BRCA)   Data format 
dense
 Configure 		 Cervical  TCGA Cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC)   Data format 
dense
 Configure 		 Colon  TCGA Colon adenocarcinoma (COAD)   Data format 
dense
 Configure 		 Glioblast.  TCGA Glioblastoma multiforme (GBM)   Data format 
dense
 Configure 		 Head and Neck  TCGA Head and Neck squamous cell carcinoma (HNSC)   Data format 
dense
 Configure 		 Kidney clear cell  TCGA Kidney renal clear cell carcinoma (KIRC)   Data format 
dense
 Configure 		 Lung  TCGA Lung adenocarcinoma (LUAD)   Data format 
dense
 Configure 		 Lung squamous  TCGA Lung squamous cell carcinoma (LUSC)   Data format 
dense
 Configure 		 Myeloid (Blood)  TCGA Acute Myeloid Leukemia (LAML)   Data format 
dense
 Configure 		 Ovarian  TCGA Ovarian serous cystadenocarcinoma (OV)   Data format 
dense
 Configure 		 Pancreatic  TCGA Pancreatic adenocarcinoma (PAAD)   Data format 
dense
 Configure 		 Prostate  TCGA Prostate adenocarcinoma (PRAD)   Data format 
dense
 Configure 		 Skin  TCGA Skin Cutaneous Melanoma (SKCM)   Data format 
dense
 Configure 		 Stomach  TCGA Stomach adenocarcinoma (STAD)   Data format 
dense
 Configure 		 Thyroid  TCGA Thyroid carcinoma (THCA)   Data format 
dense
 Configure 		 Uterine Corpus  TCGA Uterine Corpus Endometrial Carcinoma (UCEC)   Data format 
    
Data schema/format description and download
Assembly: Human Feb. 2009 (GRCh37/hg19)

Description

The Cancer Genome Atlas is a NIH-funded project to catalog genetic mutations responsible for cancer. It is sequencing 25 tumor types, twelve are already part of the Pan-Cancer data collection shown here.

The mutations are separated by tumor type and annotated with mutation impact. You can mouse over tracks to see the complete description of the tumor type.

For questions or feedback on the data, please contact the National Cancer Institute Center for Bioinformatics at ncicbiit@mail.nih.gov.

Methods

TCGA somatic mutations in MAF format were downloaded from Synapse and converted to VCF following the instructions provided by Cyriac Kandoth on BioStars.org. The resulting VCFs were split by sample and merged again by project with VCF-tools. Conversion and formatting by Maximilian Haeussler.

Credits

Data shown here are in whole based upon data generated by the TCGA Research Network: http://cancergenome.nih.gov/.