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Yossi Farjoun 25fa25b618 Added option to validate gvcf (for ValidateVariants) (#1379) 
* with option --gvcf CLP will now put extra checks that a gvcf must adhere to (existance of <NON_REF> allele at every variant, and that the variants in total cover the entire requested intervals, or the whole genome if no intervals have been specified)
* works on gvcf produced by HC when using either GVCF or BP_RESOLUTION mode
* added positive and negative tests
 		2016-05-26 06:42:45 -04:00
..
VectorPairHMM Update licenses 2016-03-05 01:09:43 -08:00
c After renaming the packages, instead of updating the JNI library used for testing bwa, moving the classes to the archive. 2014-05-19 17:36:41 -04:00
chainFiles The contig is named MT not M in b36. Delivers PT68890442. 2014-04-08 10:03:47 -04:00
doc Updated readme in public/doc to just point to the website 2015-03-12 11:52:48 -04:00
external-example Move htsjdk and picard to version 2.3.0 2016-05-16 14:50:00 -04:00
gatk-engine Move htsjdk and picard to version 2.3.0 2016-05-16 14:50:00 -04:00
gatk-queue Update licenses 2016-03-05 01:09:43 -08:00
gatk-queue-extensions-generator Adding OtherArgumentRequired option to allow an argument to require an additional argument. 2016-05-17 16:31:41 -04:00
gatk-queue-extensions-public Yf tumor only (#1298) 2016-05-12 15:26:04 -04:00
gatk-root Move htsjdk and picard to version 2.3.0 2016-05-16 14:50:00 -04:00
gatk-tools-public Added option to validate gvcf (for ValidateVariants) (#1379) 2016-05-26 06:42:45 -04:00
gatk-utils Added option to validate gvcf (for ValidateVariants) (#1379) 2016-05-26 06:42:45 -04:00
gsalib Update pom versions to mark the start of GATK 3.6 development 2015-11-25 01:52:51 -05:00
java/config Refactored maven directories and java packages replacing "sting" with "gatk". 2014-05-19 17:36:39 -04:00
package-tests Update pom versions to mark the start of GATK 3.6 development 2015-11-25 01:52:51 -05:00
repo Move htsjdk and picard to version 2.3.0 2016-05-16 14:50:00 -04:00
src/main Added faster built executable, non-packaged jars. 2014-11-05 00:30:46 +08:00
pom.xml Update pom versions to mark the start of GATK 3.6 development 2015-11-25 01:52:51 -05:00