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Eric Banks d689f61005 Fixed up some of the genotype-level annotations being propogated in the single sample HC pipeline. 
1. AD values now propogate up (they weren't before).
2. MIN_DP gets transferred over to DP and removed.
3. SB gets removed after FS is calculated.

Also, added a bunch of new integration tests for GenotypeGVCFs.
 		2014-02-07 12:47:54 -05:00
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c At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings. 2012-01-17 14:47:53 -05:00
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doc Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs) 2013-03-12 10:57:14 -04:00
external-example Added a set of serial tests to gatk/queue packages, which runs all tests under their package in one TestNG execution. 2014-02-06 08:25:38 -05:00
gatk-framework Fixed up some of the genotype-level annotations being propogated in the single sample HC pipeline. 2014-02-07 12:47:54 -05:00
gatk-package Packages link private/testdata, so that mvn test -Dsting.serialunittests.skipped=false works. 2014-02-06 08:25:38 -05:00
gatk-queue-extgen Bumped version to 2.8-SNAPSHOT, using new update_pom_versions.sh script. 2014-02-03 13:50:46 -05:00
gsalib Added a set of serial tests to gatk/queue packages, which runs all tests under their package in one TestNG execution. 2014-02-06 08:25:38 -05:00
java/config Moved files to maven directories. 2014-02-03 13:50:44 -05:00
package-tests Added a set of serial tests to gatk/queue packages, which runs all tests under their package in one TestNG execution. 2014-02-06 08:25:38 -05:00
perl Fixing the liftover script to not require strict VCF header validation. 2013-11-07 09:02:17 -05:00
queue-framework Added a set of serial tests to gatk/queue packages, which runs all tests under their package in one TestNG execution. 2014-02-06 08:25:38 -05:00
queue-package Packages link private/testdata, so that mvn test -Dsting.serialunittests.skipped=false works. 2014-02-06 08:25:38 -05:00
repo Added a set of serial tests to gatk/queue packages, which runs all tests under their package in one TestNG execution. 2014-02-06 08:25:38 -05:00
sting-root Rev Picard (public) to 1.107.1676 2014-02-04 22:04:28 -05:00
sting-utils Added a set of serial tests to gatk/queue packages, which runs all tests under their package in one TestNG execution. 2014-02-06 08:25:38 -05:00
pom.xml Bumped version to 2.8-SNAPSHOT, using new update_pom_versions.sh script. 2014-02-03 13:50:46 -05:00