From 6d21143f763a0a3a5098acb5698cb549f37a6db5 Mon Sep 17 00:00:00 2001 From: Tom Clegg Date: Wed, 11 Dec 2013 20:10:53 -0800 Subject: [PATCH] Rename annotation DepthOfCoverage to Coverage GATK 2.6-4-g3e5ff60 says: Annotation DepthOfCoverage is no longer available in the GATK; it has been deprecated since version 2.4 (renamed to Coverage) --- crunch_scripts/GATK2-merge-call | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/crunch_scripts/GATK2-merge-call b/crunch_scripts/GATK2-merge-call index c58444909f..be204404fb 100755 --- 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', 'DepthOfCoverage', + '-A', 'Coverage', '-A', 'AlleleBalance', '-A', 'QualByDepth', '-A', 'HaplotypeScore', -- 2.30.2