Genome Analysis Toolkit

[Chris Goodman]

Here are the references for the Broad Institute Genome Analysis
Toolkit:
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-
generation DNA sequencing data.
McKenna AH, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A,
Garimella K, Altshuler D, Gabriel S, Daly M, Depristo M.
Genome Res. 2010 Jul 19. [Epub ahead of print]
PMID: 20644199 [PubMed - as supplied by publisher]

Link to
The Genome Analysis Toolkit - GSA
http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit


For your review - any comments?

[Chris Goodman]

There is also a Java Style guide for coding standards by the Broad
institute for the GATK
http://www.broadinstitute.org/gsa/wiki/images/8/86/GATKCodingStandards.pdf
and
http://www.broadinstitute.org/gsa/wiki/index.php/Coding_standards

> The Genome Analysis Toolkit - GSAhttp://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_...

[ffoe...@gmail.com]

Hi Chris,

Thanks for sharing this. My company, Genus, does a lot of research on SNP data, mainly population based statistical methods. We'd like to incorporate porcine/bovine genomes into our analysis at some point... have you had experience with GATK?

Fernanda