diff --git a/packages/CreatePackager.xsl b/packages/CreatePackager.xsl new file mode 100644 index 000000000..3fa71070e --- /dev/null +++ b/packages/CreatePackager.xsl @@ -0,0 +1,83 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/packages/ReadQualityRecalibrator.xml b/packages/ReadQualityRecalibrator.xml new file mode 100644 index 000000000..02b23face --- /dev/null +++ b/packages/ReadQualityRecalibrator.xml @@ -0,0 +1,20 @@ + + + ReadQualityRecalibrator + org.broadinstitute.sting.gatk.CommandLineGATK + + org.broadinstitute.sting.playground.gatk.walkers.CovariateCounterWalker + org.broadinstitute.sting.playground.gatk.walkers.LogisticRecalibrationWalker + + + python/RecalQual.py + python/LogisticRegressionByReadGroup.py + + + R/logistic_regression.R + /humgen/gsa-scr1/GATK_Data/dbsnp_129_b36.rod + /broad/1KG/reference/human_b36_both.fasta + /broad/1KG/reference/human_b36_both.dict + /broad/1KG/reference/human_b36_both.fasta.fai + +