Ami Levy-Moonshine c5fc5c4f8c create 2 new tools: ... - ASEReadCounter (public tool) replce Tuuli's script to produce the input to Manny's tool. It count the number of reads that support the ref allele and the alt allele, filtereing low qual reads and bases and keep only properPaired reads - ASECaller (private tool) take both RNA and DNA, and produce ontingencyTables ** still under development ** minor changes in other tools: - update RNA HC variant calling scala script - expose FS method pValueForContingencyTable to be able to call it from ASEcaller In ASEReadCounter: - allow different option to deal with overlaping read from the same fragment - add option to ignore or include indels in the pileups - add option to disabled DuplicateRead add ASEReadCounterIntegrationTest.java and files for the test		2015-03-21 16:56:00 -04:00
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gatk-package-distribution	Added faster built executable, non-packaged jars.	2014-11-05 00:30:46 +08:00
gatk-queue-extensions-distribution	Regression: The new 'includeUnmapped' PartitionBy annotation was incorrectly set for HC	2015-03-13 00:24:57 -04:00
gatk-queue-package-distribution	Added faster built executable, non-packaged jars.	2014-11-05 00:30:46 +08:00
gatk-tools-protected	create 2 new tools:	2015-03-21 16:56:00 -04:00
pom.xml	Update pom versions to mark the start of GATK 3.4 development	2014-10-23 22:31:44 -04:00