Guillermo del Angel c9d3c67a9b Small Queue/scala improvements, and commiting pipeline scripts developed for ancient DNA processing for posterity: ... -- Picard extension so Queue scripts can use FastqToSam -- Single-sample BAM processing: merge/trim reads + BWA + IR + MD + BQSR. Mostly identical to standard pipeline, except for the adaptor trimming/merging which is critical for short-insert libraries. -- Single-sample calling (experimental, work in progress): standard UG run but outputting at all sites, meant for deep whole genomes. New scripts		2013-04-08 11:52:13 -04:00
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R	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -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	Fix caching indices in the PairHMM	2013-04-08 11:05:12 -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	Small Queue/scala improvements, and commiting pipeline scripts developed for ancient DNA processing for posterity:	2013-04-08 11:52:13 -04:00
testdata	Reverting move of BQSR tests to public, as per DR's email	2012-07-19 10:02:05 -04:00