Mauricio Carneiro e991307eb5 Including SplitByRG in the FullProcessingPipeline ... Why wasn't it there before, you ask ---------------------------------- Before I was running it separately (by hand), but now it's integrated in the FullProcessingPipeline. Integration was a pain because of Queue's limitation of only allowing 1 @Output file. This forced me to write the ugliest piece of code of my life, but it's working and it's processing the YRI from scratch using that right now. So I'm happy... somewhat. Other changes to the pipeline ----------------------------- * Add --filter_bases_not_stored to the IndelRealigner step -- sometimes BAM files have reads with no bases stored in the unmapped section (no idea why) but this disrupts the pipeline. * Change adaptor marking parameter to "dual indexed" instead of "pair-ended" -- for PCR Free data.		2013-08-18 00:51:32 -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	Merge pull request #380 from broadinstitute/gg_gatkdocs_arglabels	2013-08-16 15:34:56 -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	Including SplitByRG in the FullProcessingPipeline	2013-08-18 00:51:32 -04:00
testdata	Walker to create a fastq file from an interval list	2013-06-29 11:24:16 -04:00