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
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main/java/org/broadinstitute/gatk	Reads are now realigned to the most likely haplotype before being used by the annotations.	2014-06-30 10:35:50 -04:00
test/java/org/broadinstitute/gatk	Reads are now realigned to the most likely haplotype before being used by the annotations.	2014-06-30 10:35:50 -04:00