Mauricio Carneiro 22d2563823 added BWA SW alignment ... The pipeline now accepts fasta/fastq files and aligns them using BWA SW, adds default basequalities, creates read groups and performs BQSR.		2011-08-09 17:05:24 -04:00
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examples	Fixed example unified genotyper pipeline to wrap filter expressions with quotes and use rod binding name "variant" instead of "vcf".	2011-08-03 02:21:01 -04:00
lib	moving the example scala scripts to the qscripts package.	2011-07-01 16:14:59 -04:00
DataProcessingPipeline.scala	removing temporary bam index	2011-08-08 10:49:28 -04:00
GATKResourcesBundle.scala	Updating resource bundle generation qscript for changeover to git	2011-08-08 12:35:39 -04:00
MethodsDevelopmentCallingPipeline.scala	Making the outputDir optional. Default = ./	2011-07-05 16:30:41 -04:00
RecalibrateBaseQualities.scala	added BWA SW alignment	2011-08-09 17:05:24 -04:00
StandardVariantEvaluation.scala	new home for the core qscripts	2011-06-30 11:32:06 -04:00