Useful Resources
Examples of complete implementations of a variant calling pipeline:
- The Broad institute WDL reference implementations of the GATK best practices- here
- The H3ABioNet CWL implementation of the best practices (GATK3.5)- here
- A configurable Swift-t implementation (different tools, versions and options can be interchanged, so it is easy to confirm to functional equivalence specifications1 )- here
The GATK Resource Bundle2
The GATK resource bundle is a collection of standard files for working with human resequencing data with the GATK. Until the Hg38 bundle is complete, the b37 resources remain the standard data. To access the bundle on the FTP server, use the following login credentials:
Location: ftp.broadinstitute.org/bundle/b37
Username: gsapubftp-anonymous
Password:
Or, simply download using:
wget -r ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/b37
Bibliography
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Regier, A. A. et al. Functional equivalence of genome sequencing analysis pipelines enables harmonized variant calling across human genetics projects. BioRxiv (2018). doi:10.1101/269316 ↩
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What’s in the resource bundle and how can I get it? — GATK-Forum. at https://gatkforums.broadinstitute.org/gatk/discussion/1213/whats-in-the-resource-bundle-and-how-can-i-get-it ↩
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