Mauricio Carneiro 765f5450ac Updated Full Processing Pipeline ... * add interleaved fastq option to sam2fastq * add optional adapter trimming path * add "skip_revert" option to skip reverting the bams (sometimes useful -- hidden parameter) * add a walker that reads in one bam file and outputs N bam files, one for each read group in the original bam. This is a very important step in any BAM reprocessing pipeline. I am using this new pipeline to process the CEU and YRI PCR Free WGS trios.		2013-08-13 23:35:32 -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	Updated Full Processing Pipeline	2013-08-13 23:35:32 -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