Khalid Shakir 0adb388dee Fixed bug in SelectVariants that was annotating sample_file / exclude_sample_file as @Argument instead of @Input meaning they weren't tracked in Queue. ... Updates for HybridSelectionPipeline: - Use VQSR on SNPs for projects using bait set whole_exome_agilent_1 and applying cut at 98.5. - If a whole_exome_agilent_1 project has less than 50 samples also mixing in 1000G samples to reach VQSR thresholds. - Updated SNP hard filters based on analysis done with ebanks to approximate VQSR results on small target batches. - Removed GSA_PRODUCTION_ONLY flag from indel caller. - Updated indel hard filters based on delangel's analysis. - Updated HybridSelectionPipelineTest to use HARD SNP filters only, for now.		2011-09-06 12:41:46 -04:00
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net/sf	Removed annoying FastaSequenceIndexBuilderProgressListener infrastructure that was just a boolean switch on whether to print progress or not.	2011-07-27 22:06:23 -04:00
org/broadinstitute/sting	Fixed bug in SelectVariants that was annotating sample_file / exclude_sample_file as @Argument instead of @Input meaning they weren't tracked in Queue.	2011-09-06 12:41:46 -04:00