Open Genomics

A whole genome sequence subclonal copy number caller

Dirichlet Process-based methods for subclonal reconstruction of tumours

Data preprocessing for DPClust

https://github.com/pathwayanddataanalysis/mutex

Build of Radia DNA/RNA alteration caller

Somatic Sniper

Build of tools from https://github.com/OpenGenomics/vcf2maf-tools/

Build of https://github.com/OpenGenomics/fpfilter-tool

Build of https://github.com/OpenGenomics/muse-tool

Build of MuTect Github jar

Broad's Indelocator

Annotates MAF file with mark file notes

Generate pileup from BAM dataset

Build of https://github.com/OpenGenomics/varscan-tool

TCGA VCF tools

Tools built from https://github.com/vcftools/vcftools

Samtools

Build of https://github.com/OpenGenomics/pindel-tool

Picard

gatk4-tool

Download files from NCI GDC

Ensembl's variant effect predictor (VEP) tool

https://github.com/OpenGenomics/gatk-cocleaning-tool

Detects samples in a MAF with over-abundance of G>T mutations compared to C>A mutations.

Genetorrent tool.

Build of https://github.com/gt1/biobambam2