Ami Levy Moonshine ef3882f439 PhaseByTransmission: small typo /n. variantCallQC_summaryTablesOnly.R: small changes (more to come) /n GeneralCallingPipeline.scala: the new pipeline script. It is not as clean as I want it to be, but it works. I still going to work on it a little bit more. Also, it does not include yet: (1) the RR step (2) need better eval step (3) need to include other targets (currently it eork on the CEU Trio)		2012-10-11 14:51:41 -04:00
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R	Fix a nasty bug in reading GATK reports with a single line	2012-09-10 20:14:13 -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	…
java	PhaseByTransmission: small typo /n. variantCallQC_summaryTablesOnly.R: small changes (more to come) /n GeneralCallingPipeline.scala: the new pipeline script. It is not as clean as I want it to be, but it works. I still going to work on it a little bit more. Also, it does not include yet: (1) the RR step (2) need better eval step (3) need to include other targets (currently it eork on the CEU Trio)	2012-10-11 14:51:41 -04:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	Removed 'Walker' suffix from packages/GATKEngine.xml that were breaking the packaged release.	2012-07-23 16:32:31 -04:00
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	Update DataProcessingPipelineTest MD5s	2012-09-24 15:38:07 -04:00
testdata	Reverting move of BQSR tests to public, as per DR's email	2012-07-19 10:02:05 -04:00