goSNAP

goSNAP is a high performance ensemble variant calling pipeline designed for large scale variant calling in next generation sequencing data. It employs multiple variant callers (currently including SNPTools, GATK-HaplotypeCaller, GATK-UnifiedGenotyper and GotCloud for SNP calling) in joint calling across thousands to millions of samples. It is highly scalable and can be deployed to different cloud computing platforms (with the version supporting DNAnexus currently released).

Installation

To build the DNAnexus App version of goSNAP, the DNAnexus commandline API (dx-toolkit) is required. Once dx-toolkit is installed, you may go to your local copy of the app directory and build the app with

$ cd gosnap.app
$ dx build -f -d TARGET_DX_PROJECT:/PATH_TO_APP/

Usage

For DNAnexus version, you may run the goSNAP App with

$ dx run TARGET_DX_PROJECT:/PATH_TO_APP/gosnap.app -idxSliceBamTar=<bam_file_tarball> -idxRefGenTar=<human_genome_reference_tarball></human_genome_reference_tarball></bam_file_tarball>

More detail usage will follow.

History

As of May 6, 2015, goSNAP SNP calling part in DNAnexus App version is released.

License

goSNAP is released under Apache 2.0 License for NON-COMMERCIAL use. For commercial use, please contact Dr. Fuli Yu @ Baylor College of Medicine (fyu@bcm.edu). For details, please see LICENSE.

TODO

goSNAP INDEL calling part and the version supporting other cloud platforms will be released later.