{ "##_COMMENT1": "Input/Output Files", "Cram2FilteredVcf.input_file": "/home/doc/Desktop/gatk_output/gatk_reference_files/NA12878.cram", "Cram2FilteredVcf.output_prefix": "hg38_20k_na12878_DOL", "##_COMMENT2": "Reference/Resource Files", "Cram2FilteredVcf.reference_fasta": "/home/doc/Desktop/gatk_output/gatk_reference_files/Homo_sapiens_assembly38.fasta", "Cram2FilteredVcf.reference_dict": "/home/doc/Desktop/gatk_output/gatk_reference_files/Homo_sapiens_assembly38.dict", "Cram2FilteredVcf.reference_fasta_index": "/home/doc/Desktop/gatk_output/gatk_reference_files/Homo_sapiens_assembly38.fasta.fai", "Cram2FilteredVcf.resource_fofn": "/home/doc/Desktop/gatk_output/gatk_reference_files/resource_fofn.txt", "Cram2FilteredVcf.resource_fofn_index": "/home/doc/Desktop/gatk_output/gatk_reference_files/resource_fofn_index.txt", "Cram2FilteredVcf.calling_intervals": "/home/doc/Desktop/gatk_output/gatk_reference_files/wgs_calling_regions.hg38.interval_list", "##_COMMENT3": "Workflow Parameters", "Cram2FilteredVcf.info_key": "CNN_2D", "Cram2FilteredVcf.snp_tranches": " --snp-tranche 99.9 ", "Cram2FilteredVcf.indel_tranches": " --indel-tranche 99.5 ", "Cram2FilteredVcf.tensor_type":"read_tensor", "Cram2FilteredVcf.extra_args": "--dont-trim-active-regions -stand-call-conf 0 -A Coverage -A ChromosomeCounts -A BaseQuality -A FragmentLength -A MappingQuality -A ReadPosition ", "Cram2FilteredVcf.scatter_count": 4, "Cram2FilteredVcf.inference_batch_size": 8, "Cram2FilteredVcf.transfer_batch_size": 32, "##_COMMENT4": "Runtime Attributes", "Cram2FilteredVcf.gatk_docker": "broadinstitute/gatk:4.1.0.0", "Cram2FilteredVcf.preemptible_attempts": 10, "Cram2FilteredVcf.mem_gb": 7 }