Ryan Poplin b22c9c2cb4 Improvements to the reference model pipeline. ... -- We use the RegenotypeVariants walker to recompute the qual field. (instead of the discussed idea of adding this functionality to CombineVariants) -- QualByDepth will now be recomputed even if the stratified contexts are missing. This greatly improves the QD estimate for this pipeline. Doesn't work for multi-allelics since the qual can't be recomputed.		2013-11-01 17:58:25 -04:00
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R	Something changed with the ggtitle syntax in the latest version of ggplot2.	2013-08-14 14:40:03 -04:00
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
chainFiles	…
doc	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
java	Improvements to the reference model pipeline.	2013-11-01 17:58:25 -04:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	ValidatingPileup was renamed to CheckPileup	2013-02-15 11:56:19 -05:00
perl	Split out contig names from Reference .fai file on white space (to support the GATK resource bundle's file human_g1k_v37.fasta.fai.gz, which does not use tab delimiters)	2012-06-07 16:56:32 -04:00
scala	Merge pull request #411 from broadinstitute/eb_add_exome_intervals_to_bundle_script	2013-10-29 07:38:44 -07:00
testdata	Walker to create a fastq file from an interval list	2013-06-29 11:24:16 -04:00