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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
..
VectorPairHMM Changed 'sting' to 'gatk' in the VectorLoglessPairHMM classes and the 2014-05-19 17:36:41 -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 Refactored maven directories and java packages replacing "sting" with "gatk". 2014-05-19 17:36:39 -04:00
external-example Revert "Appending to md5db in the gatkdir, with additional logging." 2014-07-11 01:11:20 +08:00
gatk-engine Bug fix for poms missing package test artifacts. 2014-07-08 06:34:26 +08:00
gatk-queue Update VQSR Rnd BQSR script generation code for compatibility with latest ggplot version. Update queueJobReport.R and public/gsalib/src/R/R/gsa.variantqc.utils.R also 2014-07-09 15:36:58 -04:00
gatk-queue-extensions-generator Refactored maven directories and java packages replacing "sting" with "gatk". 2014-05-19 17:36:39 -04:00
gatk-queue-extensions-public Refactored DoC custom Queue wrappers to a non-package object. 2014-06-26 00:59:18 +08:00
gatk-root Revert "Appending to md5db in the gatkdir, with additional logging." 2014-07-11 01:11:20 +08:00
gatk-tools-public Various documentation improvements 2014-07-14 12:03:03 -04:00
gatk-utils Bug fix for poms missing package test artifacts. 2014-07-08 06:34:26 +08:00
gsalib Update VQSR Rnd BQSR script generation code for compatibility with latest ggplot version. Update queueJobReport.R and public/gsalib/src/R/R/gsa.variantqc.utils.R also 2014-07-09 15:36:58 -04:00
java/config Refactored maven directories and java packages replacing "sting" with "gatk". 2014-05-19 17:36:39 -04:00
package-tests Refactored maven directories and java packages replacing "sting" with "gatk". 2014-05-19 17:36:39 -04:00
perl Fixing the liftover script to not require strict VCF header validation. 2013-11-07 09:02:17 -05:00
repo Refactored maven directories and java packages replacing "sting" with "gatk". 2014-05-19 17:36:39 -04:00
src/main/scripts/shell For now, executing the delete_maven_links.sh just ahead of creating the symbolic links during the process-test-resources phase. 2014-06-25 02:32:15 +08:00
pom.xml Refactored maven directories and java packages replacing "sting" with "gatk". 2014-05-19 17:36:39 -04:00