Remove GIAB annotation parameters

BD2KGenomics · Jul 2, 2016 · b8bcde7 · b8bcde7
1 parent 16bdfaf
commit b8bcde7
Showing 1 changed file with 2 additions and 9 deletions.
diff --git a/src/toil_scripts/gatk_germline/germline.py b/src/toil_scripts/gatk_germline/germline.py
@@ -181,17 +181,10 @@ def gatk_haplotype_caller(job, bam_id, bai_id, config):
                '-variant_index_parameter', '128000',
                '--genotyping_mode', 'Discovery',
                '--emitRefConfidence', 'GVCF',
-               '--annotation', 'LowMQ',
-               '--annotation', 'Coverage',
                '--annotation', 'QualByDepth',
-               '--annotation', 'FisherStrand',
-               '--annotation', 'HomopolymerRun',
-               '--annotation', 'StrandOddsRatio',
                '--annotation', 'DepthPerSampleHC',
-               '--annotation', 'RMSMappingQuality',
-               '--annotation', 'ReadPosRankSumTest',
-               '--annotation', 'ClippingRankSumTest',
-               '--annotation', 'BaseQualityRankSumTest']
+               '--annotation', 'FisherStrand',
+               '--annotation', 'ReadPosRankSumTest']
 
     if config['unsafe_mode']:
         command = ['-U', 'ALLOW_SEQ_DICT_INCOMPATIBILITY'] + command