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
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gatk-package-distribution	Update pom versions to mark the start of GATK 3.5 development	2015-05-15 00:44:54 -04:00
gatk-queue-extensions-distribution	Update pom versions to mark the start of GATK 3.5 development	2015-05-15 00:44:54 -04:00
gatk-queue-package-distribution	Update pom versions to mark the start of GATK 3.5 development	2015-05-15 00:44:54 -04:00
gatk-tools-protected	Enable contamination correction via downsampling (as for HaplotypeCaller), added test	2015-06-15 07:59:15 -04:00
pom.xml	Update pom versions to mark the start of GATK 3.5 development	2015-05-15 00:44:54 -04:00