chiotti

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

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

Build of MuTect Github jar

Somatic Sniper

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

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

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

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

Generate pileup from BAM dataset

Build of Radia DNA/RNA alteration caller

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

Download files from NCI GDC

Samtools

TCGA VCF tools

Broad's Indelocator

Picard

Docker image that provides the TrimGalore trimming software