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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R	queueJobReport is a public feature of Queue	2011-08-29 17:20:54 -04:00
c	Reinitialize random seed in the bwa bindings from the fixed seed stored in the	2011-07-22 13:41:53 -04:00
chainFiles	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
doc	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
java	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
packages	Added edu.mit.broad.picard to Queue packaged jar.	2011-07-23 14:40:29 -04:00
perl	Moving these supported perl scripts to public	2011-07-01 17:26:25 -04:00
scala	Allowing multiple dnsnp and indel files in the DPP	2011-09-02 13:38:47 -04:00
testdata	GZIP VCF for testing	2011-08-19 09:05:39 -04:00