Data Processing

The GDC MAF tool aggregates aliquot-level MAFs, which originate from one tumor-normal pair. MAFs can aggregated on a project-level or by providing a set of files/cases. Note that currently the GDC MAF tool only supports Ensemble aliquot-level MAFs generated from whole exome sequencing. Ensemble aliquot-level MAFs include variants from all five variant callers (MuTect2, MuSE, Varscan2, Pindel) and include information about which caller each variant originated from. The GDC MAF tool will only aggregate MAFs from within one GDC project.

Tool suite for analyzing high throughput bisulfite sequencing data.

BISCUIT performs:

• Alignment and quality control of bisulfite sequencing reads
• Extraction of DNA methylation level
• Extraction of genetic information from bisullfite-sequencing data 
• Analysis of allele-specific methylation and methylation haplotype

Tool for analyzing Infinium DNA methylation array data.

The SeSAME Tool:

• Reduction to artifactual detection from Infinium of DNA methylation microarrays
• Low-level processing of Illumina Infinium DNA methylation array
• Quality control of DNA methylation arrays
• Biological inference (sex, age, karyotypes, copy number, etc.)