Valentin Ruano-Rubio 311b6815b3 Fixed the QUAL calculation of the EXACT_INDEPENDENT. ... The QUAL value calculated by this Exact AF Calculator is very underestimated when there are more than one alternative allele (non-biallelic sites). The reason is that the QUAL was roughly calculated by adding the QUALs resulting of each alternative alleles vs all other alleles, reference and alts, collapsed. This is ok for MLEAC calculations but not for QUAL. Now, for calculating the QUAL we collapse all the alternatives as only one. This change improves sensitivy with a cost of additional false positives, but this is naturally expected. The resulting QUAL column is much closer to the one returned by the reference implementation. Story: https://www.pivotaltracker.com/story/show/75926368. Changes: Changed the QUAL calculation as described above. Updated MD5s. Fixed MD5s		2014-09-29 11:04:52 -04:00
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gatk-package-distribution	Now passing in the path to the GATK directory to tests.	2014-09-02 01:40:59 +08:00
gatk-queue-extensions-distribution	Now passing in the path to the GATK directory to tests.	2014-09-02 01:40:59 +08:00
gatk-queue-package-distribution	Now passing in the path to the GATK directory to tests.	2014-09-02 01:40:59 +08:00
gatk-tools-protected	Fixed the QUAL calculation of the EXACT_INDEPENDENT.	2014-09-29 11:04:52 -04:00
pom.xml	Update pom versions to mark the start of GATK 3.3 development	2014-07-17 12:09:33 -04:00