Tools related to GATK
Tools developed by other groups
MuTect v1 -- Reliable and accurate identification of somatic point mutations in high-throughput sequencing data of cancer genomes. Note that a new version called MuTect2 has been integrated into the GATK as of version 3.5 as a beta preview. Once MuTect2 moves out of beta status, support for the original MuTect will be discontinued. You can find the MuTect2 tool doc at https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_cancer_m2_MuTect2.php
ReCapSeg is a tool for performing analysis of somatic Copy Number Variation. Note that this version of the tools (implemented in Python) is being replaced by a new version (implemented in Java) that is now available in the GATK 4 alpha preview. See http://gatkforums.broadinstitute.org/categories/gatk-4-alpha for documentation on the new CNV workflow.
Oncotator is a tool for annotating human genomic point mutations and indels with data relevant to cancer researchers. Ask your questions about Oncotator here.
Genome STRiP (Genome STRucture In Populations) -- Tools for discovering and genotyping structural variations using sequencing data. See http://www.broadinstitute.org/software/genomestrip/ for more details.
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