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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R	Removed plots generation from the BaseRecalibration software	2013-06-19 14:47:56 -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	Disabled emission of doc URLs for external codecs to avoid broken links	2013-08-10 10:04:04 -07:00
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	Updated Full Processing Pipeline	2013-08-13 23:35:32 -04:00
testdata	Walker to create a fastq file from an interval list	2013-06-29 11:24:16 -04:00