bigdatagenomics/avocado — pull request #76 by fnothaft (2014-06-04 17:22:30+00:00)
Title: Adding generic stub for external variant callers.

Adds a generic hook for calling out to external variant callers. Currently, this assumes that the variant callers take sorted, streaming BAM input, and write VCF to a file. The stage is configured by setting the "command" parameter, which is the command to run, and by setting the "partitions" parameter, which is the number of partitions to use during the map phase. In the command, the string "::VCFOUT::" will be replaced by the local path to the VCF output file on each node.