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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cancer	Updating licenses for all scala files	2013-01-10 17:46:10 -05:00
gatk	change the default VCFs gatherer of the GATK (not just the UG)	2013-01-18 15:03:12 -05:00
picard	Small Queue/scala improvements, and commiting pipeline scripts developed for ancient DNA processing for posterity:	2013-04-08 11:52:13 -04:00
samtools	Updating licenses for all scala files	2013-01-10 17:46:10 -05:00
snpeff	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00