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Add command-line flags. (refs #2463)
[arvados.git]
/
crunch_scripts
/
GATK2-merge-call
diff --git
a/crunch_scripts/GATK2-merge-call
b/crunch_scripts/GATK2-merge-call
index be204404fb9e8ed239c1934895713fea311b4b9a..c58444909f7678bfa1fe4cf42d8719741039c7f6 100755
(executable)
--- a/
crunch_scripts/GATK2-merge-call
+++ b/
crunch_scripts/GATK2-merge-call
@@
-200,7
+200,7
@@
arvados_gatk2.run(
'-o', os.path.join(tmpdir, 'out.vcf'),
'--dbsnp', os.path.join(bundle_dir, 'dbsnp_137.b37.vcf'),
'-metrics', 'UniGenMetrics',
- '-A', 'Coverage',
+ '-A', '
DepthOf
Coverage',
'-A', 'AlleleBalance',
'-A', 'QualByDepth',
'-A', 'HaplotypeScore',