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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
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depristo 2010-12-01 14:57:14 +00:00
parent 0892daddb0
commit 984e94521e
1 changed files with 9 additions and 1 deletions
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10
python/dataProcessingPaper.py
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@ -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