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gatk-3.8/protected/java/test/org/broadinstitute/sting/gatk/walkers
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Mark DePristo 209dd64268 HaplotypeCaller now emits per-sample DP 
-- Created a new annotation DepthPerSampleHC that is by default on in the HaplotypeCaller
-- The depth for the HC is the sum of the informative alleles at this site.  It's not perfect (as we cannot differentiate between reads that align over the event but aren't informative vs. those that aren't even close) but it's a pretty good proxy and it matches with the AD field (i.e., sum(AD) = DP).
-- Update MD5s
-- delivers [#48240601]
 		2013-06-06 09:47:32 -04:00
..
annotator Update expected test output for Java 7 2013-05-01 16:18:01 -04:00
beagle Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
bqsr Make BQSR calculateIsIndel robust to indel CIGARs are start/end of read 2013-05-31 13:58:37 -04:00
compression/reducereads Fix error in merging code in HC 2013-05-31 16:29:29 -04:00
diagnostics Update MD5s and the Diagnose Target scala script 2013-05-13 12:06:17 -04:00
diffengine Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs) 2013-03-12 10:57:14 -04:00
fasta Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
filters Don't allow users to specify keys and IDs that contain angle brackets or equals signs (not allowed in VCF spec). 2013-04-05 00:52:32 -04:00
genotyper Bugfix for bad AD values in UG/HC 2013-06-05 17:48:41 -04:00
haplotypecaller HaplotypeCaller now emits per-sample DP 2013-06-06 09:47:32 -04:00
indels Secondary alignments were not handled correctly in IndelRealigner 2013-05-06 19:09:10 -04:00
phasing Updated all JAVA file licenses accordingly 2013-01-10 17:06:41 -05:00
validation MathUtils.randomSubset() now uses Collections.shuffle() (indirectly, through the other methods 2013-03-29 14:52:10 -04:00
varianteval Move some VCF/VariantContext methods back to the GATK based on feedback 2013-01-29 16:56:55 -05:00
variantrecalibration Update MD5s for VQSR header change 2013-04-16 11:45:45 -04:00
variantutils CombineVariants no longer adds PASS to unfiltered records 2013-05-20 16:53:51 -04:00