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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qscript	GenotypeAndValidate version 2, ready to be used.	2011-03-22 20:18:02 +00:00
src/org/broadinstitute/sting	Using an embedded version of Picard for merging un-indexed bam files after scatter/gather instead of requiring the QScripts to specify the picard JAR. May do this for the GATK jar too.	2011-03-21 18:20:01 +00:00
test/org/broadinstitute/sting/queue	While generating YAML now warning and skipping TSV rows that don't have all values.	2011-02-25 20:50:03 +00:00