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