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Ryan Poplin 0127799cba Reads are now realigned to the most likely haplotype before being used by the annotations. 
-- AD,DP will now correspond directly to the reads that were used to construct the PLs
-- RankSumTests, etc. will use the bases from the realigned reads instead of the original alignments
-- There is now no additional runtime cost to realign the reads when using bamout or GVCF mode
-- bamout mode no longer sets the mapping quality to zero for uninformative reads, instead the read will not be given an HC tag
 		2014-06-30 10:35:50 -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 Refactored maven directories and java packages replacing "sting" with "gatk". 2014-05-19 17:36:39 -04:00
gatk-engine Refactored maven directories and java packages replacing "sting" with "gatk". 2014-05-19 17:36:39 -04:00
gatk-queue Refactored maven directories and java packages replacing "sting" with "gatk". 2014-05-19 17:36:39 -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 Refactored maven directories and java packages replacing "sting" with "gatk". 2014-05-19 17:36:39 -04:00
gatk-tools-public Reads are now realigned to the most likely haplotype before being used by the annotations. 2014-06-30 10:35:50 -04:00
gatk-utils Changed 'sting' to 'gatk' in the VectorLoglessPairHMM classes and the 2014-05-19 17:36:41 -04:00
gsalib Refactored maven directories and java packages replacing "sting" with "gatk". 2014-05-19 17:36:39 -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