Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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.php187 discussions 699 comments Most recent: Mutect Analysis without a paired tumour normal & Analysis Criteria by LaboBernard on July 3Child Categories: MuTect v1 Documentation
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.17 discussions 27 comments Most recent: Buy passport online Buy an identity card online Buy driver's license online Buy the residence permit by markweber on June 14Child Categories: ReCapSeg Documentation
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.540 discussions 1.2K comments Most recent: Buy passport online Buy an identity card online Buy driver's license online by markweber on June 14Child Categories: GenomeSTRiP Documentation
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