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Laura Gauthier ce5ecf1383 Enable contamination correction via downsampling (as for HaplotypeCaller), added test 
Add oxoG read count annotation and add as default annotation
Add ##SAMPLE VCF header line in accordance with TCGA VCF spec, specifying "File" line in sample header with BAM file name and "SampleName" with BAM sample name (Don't print sample file path if --no_cmdline_in_header is specified to help with test consistency)
Turn on active region assembly-based physical phasing for M2
Clean up M2-related annotations so UG doesn't crash if M2 annotations are called
 		2015-06-15 07:59:15 -04:00
..
VectorPairHMM Update pom versions to mark the start of GATK 3.5 development 2015-05-15 00:44:54 -04:00
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 Update pom versions to mark the start of GATK 3.5 development 2015-05-15 00:44:54 -04:00
gatk-engine Add spannning deletions allele 2015-06-12 16:43:06 -04:00
gatk-queue fix typo in queue arguments 2015-06-05 17:06:23 -04:00
gatk-queue-extensions-generator Update pom versions to mark the start of GATK 3.5 development 2015-05-15 00:44:54 -04:00
gatk-queue-extensions-public Update pom versions to mark the start of GATK 3.5 development 2015-05-15 00:44:54 -04:00
gatk-root Add spannning deletions allele 2015-06-12 16:43:06 -04:00
gatk-tools-public User (mnw21cam) patch to fix DoC slowdown in 3.4 2015-06-05 21:12:46 -04:00
gatk-utils Enable contamination correction via downsampling (as for HaplotypeCaller), added test 2015-06-15 07:59:15 -04:00
gsalib Update pom versions to mark the start of GATK 3.5 development 2015-05-15 00:44:54 -04:00
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 3.5 development 2015-05-15 00:44:54 -04:00
perl Fixing the liftover script to not require strict VCF header validation. 2013-11-07 09:02:17 -05:00
repo Rev htsjdk to version 1.132 and picard to version 1.131, and switch to using the versions in maven central 2015-05-14 15:26:23 -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 3.5 development 2015-05-15 00:44:54 -04:00