Eric Banks 5ea7cd6dcc Updating resource bundle: no reason to include both genotype and sites files for Omni and HM3, sites are enough. Also, don't include duplicate entry for the Mills indels.		2012-08-31 14:01:54 -04:00
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examples	Added setupRetry() to modify jobs when Queue is run with '-retry' and jobs are about to restart after an error.	2012-08-13 15:43:05 -04:00
lib	Mostly small changes to my own scala scripts: .vcf.gz compatibility for output files, smarter beagle generation, simple script to scatter-gather combine variants. Whole genome indel calling now uses the gold standard indel set.	2012-02-22 17:20:04 -05:00
DataProcessingPipeline.scala	Disabling indel quals in BaseRecalibrator as it should be, not PrintReads.	2012-08-01 09:23:04 -04:00
GATKResourcesBundle.scala	Updating resource bundle: no reason to include both genotype and sites files for Omni and HM3, sites are enough. Also, don't include duplicate entry for the Mills indels.	2012-08-31 14:01:54 -04:00
MethodsDevelopmentCallingPipeline.scala	Turning off PHONE HOME option in the MDCP	2012-01-27 11:13:30 -05:00
PacbioProcessingPipeline.scala	Disabling indel quals in BaseRecalibrator as it should be, not PrintReads.	2012-08-01 09:23:04 -04:00