Service notice: Several of our team members are on vacation so service will be slow through at least July 13th, possibly longer depending on how much backlog accumulates during that time. This means that for a while it may take us more time than usual to answer your questions. Thank you for your patience.
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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