GATK Support Forum

Category List

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  Announcements

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

  267 discussions 1K comments Most recent: Funcotator: Functional annotation out of beta by joseph7e on September 6 September 6
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  Ask the GATK team

  Errors, bugs, problems and usage questions. This forum is maintained by support staff who answer questions with assistance from the developers of the GATK

  17.1K discussions 44.3K comments Most recent: Indel normalization + left alignment for VQSR by Kousik on 9:37AM 9:37AM
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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.

  141 discussions 752 comments Most recent: (How to) Call somatic mutations using GATK4 Mutect2 by syer89 on September 19 September 19

  Child Categories: Best Practices Workflows, Methods and Algorithms, Tutorials, Dictionary, Frequently Asked Questions, Solutions to Problems, Computing Platforms
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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.

  196 discussions 4.3K comments Most recent: At what point should I merge read group BAM files belonging to the same sample into a single file? by Lufpa on September 3 September 3

  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.

  671 discussions -36 comments Most recent: Are there any default --contig-ploidy-priors available? by slee on August 25 August 25
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  Tools related to GATK

  Tools developed by other groups

  784 discussions 2.2K comments Most recent: Web-based Oncotator server by bhanuGandham on September 20 September 20

  Child Categories: MuTect v1, ReCapSeg, Oncotator , GenomeSTRiP