carneiro 28149e5c5e GenotypeAndValidate version 2, ready to be used. ... - now it differentiates between confident REF calls and not confident calls. - you can now use a BAM file as the truth set. - output is much clearer now dataProcessingPipeline version 2, ready to be used. - All the processing is now done at the sample level - Reads the input bam file headers to combine all lanes of the same sample. - Cleaning is now scattered/gathered. Inteligently breaks down in as many intervals as possible, given the dataset. - Outputs one processed bam file per sample (and a .list file with all processed files listed) - Much faster, low pass (read Papuans) can run in the hour queue. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5493 348d0f76-0448-11de-a6fe-93d51630548a		2011-03-22 20:18:02 +00:00
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dataProcessing.scala	pacbio calling pipeline also using VQSR2 now, minor updates on the other pipelines to get the papuans through.	2011-03-18 22:06:52 +00:00
dataProcessingV2.scala	GenotypeAndValidate version 2, ready to be used.	2011-03-22 20:18:02 +00:00
justClean.scala	helper script to the papuan processing... minor updates	2011-03-22 14:11:02 +00:00
pbCalling.scala	pacbio calling pipeline also using VQSR2 now, minor updates on the other pipelines to get the papuans through.	2011-03-18 22:06:52 +00:00