Geraldine Van der Auwera a6f632874b Various documentation improvements ... - Edited intervals merging docs for correctness & clarity - Edited VQSR arg docs and made mode required (+added -mode SNP to VQSR tests) - Moved PaperGenotyper to Toy Walkers to declutter the actually useful docs - Moved GenotypeGVCFs to Variant Discovery category and clarified a few points - Clarified that the -resource argument depends on using the -V:tag format - Clarified how the pcr indel model works - Added caveat for -U ALLOW_N_CIGAR_READS - Added MathJax support for displaying equations in GATKDocs - Updated HC example commands and caveats		2014-07-14 12:03:03 -04:00
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gatk-package-distribution	Added cofoja to the gatk packages for tests to pass.	2014-07-11 23:19:42 +08:00
gatk-queue-extensions-distribution	Disabled ExampleUG Queue Tests, fixed internal extensions dependency.	2014-05-27 16:16:53 -04:00
gatk-queue-package-distribution	If passed -Pgsadev, don't build the distribution package.	2014-06-10 23:33:33 -04:00
gatk-tools-protected	Various documentation improvements	2014-07-14 12:03:03 -04:00
pom.xml	Refactored maven directories and java packages replacing "sting" with "gatk".	2014-05-19 17:36:39 -04:00