gatk3的最后一个经典版本3.8

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
public	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
settings	Reving Tribble to 23	2011-09-01 10:43:03 -04:00
LICENSE	One last test...	2011-06-28 19:18:17 -04:00
build.xml	Enable conditional inclusion of documentation for hidden features in GATKDocs.	2011-08-27 03:38:01 -04:00
ivy.xml	The tribble dependency is now handled through ivy. Revved tribble to r18 and removed obsolete build targets in build.xml	2011-08-11 16:38:29 -04:00