2 Commits (b4a2112a0dfa5c33cc4bf2814cd15364fe50e961)

Author	SHA1	Message	Date
carneiro	9e93091e9a	-baqGOP now takes phred scaled scores instead of probabilities in the command line. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4982 348d0f76-0448-11de-a6fe-93d51630548a	2011-01-13 00:06:38 +00:00
carneiro	5e9a8f9cb3	Implemented a new argument (-DQS --defaultQualityScore) that allows GATK to deal with BAM files missing quality scores. If a value is specified, all reads are filled with the default quality score. Appropriate exception is thrown if -DQS is not provided and BAM file doesn't have quality scores for every base. ... Adding the first version of the techdev pipeline (tdPipeline) git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4943 348d0f76-0448-11de-a6fe-93d51630548a	2011-01-05 22:25:08 +00:00