multithreaded GATK local realignment

[leecbaker]

OpenGE 0.2 Release

We're pleased to announce the release of OpenGE 0.2 .

Major highlights include:
* Local realignment function. This function realigns reads near indels, using all reads in the region around the indel to find a better alignment for reads. Functionality should be equivalent to GATK's IndelRealigner, but with quicker execution on multicore machines. Some datasets may be up to 12x faster.
* Added functionality to support traceability. When OpenGE performs any operation on a BAM or SAM file, it adds a record to the header of the file describing the command line options used. To review how a file was generated, you can use the new history command.
* Added the 'compare' command to compare BAM/SAM files, and identify differences.
* Many additional bug fixes.

More details are available in the change log included with the binary downloads, and in the command documentation. Source code is available at the OpenGE Github repository.

We welcome any comments and suggestions about improving OpenGE, either via this forum or via email.

[adaptivegenome]

We have a preliminary implementation of the local realignment process in GATK 1.X (now its called GATK-lite?).

Running on a single core, our implementation is 5-20% faster (the gain increases with file size). Using the AMD 16-core Opteron processors we get up to 5X speed increase. Our principle bottleneck right now is I/O (which we are resolving with advice from Nils, thanks!). The code should be considered experimental so don't add to your production pipelines just yet.

A stable release should be available in the next week or two when we formally push version 0.2 of OpenGE to GitHub. To use the experimental realignment method, you need to build OpenGE from source (we have not updated binaries yet):

http://www.github.com/adaptivegenome/openge

Any feedback or suggestions would be greatly appreciated. Particularly suggestions for future features and development.