Forum Login Issue:
Currently the "Log in with Google" button redirects you to a "Page not found." Our forum vendors have implemented a fix, and now we are just waiting on a patch to be released. In the meantime, while on the "Page not found" you can edit the URL to delete the second gatk, firecloud, or wdl (depending on what subforum you are acessing).
ex: https://gatkforums.broadinstitute.org/gatk/gatk/entry/...

GATK Support Forum

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Announcements

Announcements regarding new tools and features, as well as user support service and forum features

235 discussions 874 comments Most recent: Off-label workflow to simply call differences in two samples by JmeAlena on 12:22AM 12:22AM
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Ask the GATK team

Errors, bugs, problems and usage questions for the developers of the GATK or the community at large

7.6K discussions 35.9K comments Most recent: Can't copy GATK tool web page URLs from browser and paste them by tedtoal on April 26 April 26
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GATK4 User Guide

This section contains the GATK4 documentation. This content is best viewed at https://software.broadinstitute.org/gatk/documentation.

119 discussions 207 comments Most recent: VCF - Variant Call Format by jshelton on April 26 April 26
Child Categories: Best Practices Workflows, Methods and Algorithms, Tutorials, Dictionary, Frequently Asked Questions, Solutions to Problems, Pipelining Options
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GATK3 User Guide

This is an exact mirror of the GATK website Guide pages, with the added possibility of commenting on the documentation articles. For detailed information about the GATK Best Practices workflows, please see https://www.broadinstitute.org/gatk/guide/best-practices.php.

195 discussions 3.9K comments Most recent: What is a GVCF and how is it different from a 'regular' VCF? by Sheila on April 25 April 25
Child Categories: Tutorials, Frequently Asked Questions, Solutions to Problems, Methods and Algorithms, Dictionary, GATK 4 Beta, Archive
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Zoo & Garden

This section is intended for discussions that are specifically about resources for analysis of non-human data.

3 discussions 11 comments Most recent: Genotype likelihoods from HapMap SNPs by shlee on March 22 March 22
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Tools related to GATK

Tools developed by other groups

505 discussions 2K comments Most recent: Invalid intervals error by lucasl on April 25 April 25
Child Categories: MuTect v1, ReCapSeg, Oncotator , GenomeSTRiP

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