From 984e94521ee74b3bc5aeaccc4283dc645a80e381 Mon Sep 17 00:00:00 2001 From: depristo Date: Wed, 1 Dec 2010 14:57:14 +0000 Subject: [PATCH] Trival changes to data processing paper python git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4762 348d0f76-0448-11de-a6fe-93d51630548a --- python/dataProcessingPaper.py | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/python/dataProcessingPaper.py b/python/dataProcessingPaper.py index bd33c1e8d..4fcd251b3 100755 --- a/python/dataProcessingPaper.py +++ b/python/dataProcessingPaper.py @@ -20,7 +20,8 @@ WE_LIST = '/seq/references/HybSelOligos/whole_exome_agilent_designed_120/whole_e WGS_FILTER = [['ABFilter', 'AB > 0.75 && DP > 40'], ['DPFilter', 'DP > 120 || SB > -0.10']] # , ['QDFilter', 'QD < 5.0 && DP > 40']] WE_FILTER = [['ESPStandard', 'AB > 0.75 || QD < 5.0 || HRun > 3 || SB > -0.10']] -UG_ARGS = "-mbq 20 -mmq 20 -stand_call_conf 50 -stand_emit_conf 10 -hets 0.78e-3 -dcov 10000 -pnrm GRID_SEARCH" +#UG_ARGS = "-mbq 20 -mmq 20 -stand_call_conf 50 -stand_emit_conf 10 -hets 0.78e-3 -dcov 10000 -pnrm GRID_SEARCH" +UG_ARGS = "-stand_call_conf 10 -stand_emit_conf 10 --downsampling_type BY_SAMPLE -dcov 1000 -hets 0.78e-3" # experimental arguments for GdA test class CallTarget: def __init__(self, name, bam, interval = '', callArgs = "", b36 = False, optimize = True, filters = [], targetTiTv = 2.07, maxClusters = 16, minQual = 300, tranchToTake = 1): @@ -132,6 +133,9 @@ def main(): parser.add_option("-t", "--target", dest="target", type="string", default=None, help="Only run jobs with names containing this string") + parser.add_option("", "--noRaw", dest="noRaw", + action="store_true", default=False, + help="Exclude raw calls from output") (OPTIONS, args) = parser.parse_args() if len(args) != 1: @@ -186,6 +190,10 @@ def main(): return name in stages for callTarget in targets: + if "raw" in callTarget.name and OPTIONS.noRaw: + print 'Skipping raw data', callTarget + continue + # setup pipeline args GATK_JAR = GATK_STABLE_JAR if ( OPTIONS.dev ): GATK_JAR = GATK_DEV_JAR