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Chris Whelan ba1d23e535 Created a new tool, SiblingIBD, which finds Identical-By-Descent regions in two siblings. 
-When parental genotypes are available, implements an HMM on genotype observations in the quartet.
   -Outputs IBD regions as well as per-site posterior probabilities of being in each IBD state.
   -Includes an experimental heuristic based mode for when parental genotypes are not available.
   -Made a method in MendelianViolation public static to reuse code.
   -Added the mockito library to private/gatk-tools-private/pom.xml
 		2014-06-13 09:41:37 -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 For XHMM and Depth-of-Coverage Qscripts, add ability for user to input sample renaming file at the GATK level using existing GATK flag (--sample_rename_mapping_file) and custom pre-processing code. For XHMM Qscript, add scatter-gather for Discovery and Genotype stages. 2014-06-09 23:49:54 -04:00
gatk-root Refactored maven directories and java packages replacing "sting" with "gatk". 2014-05-19 17:36:39 -04:00
gatk-tools-public Created a new tool, SiblingIBD, which finds Identical-By-Descent regions in two siblings. 2014-06-13 09:41:37 -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
pom.xml Refactored maven directories and java packages replacing "sting" with "gatk". 2014-05-19 17:36:39 -04:00