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processing-for-variant-discovery-gatk4.b37.wgs.inputs.json
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{
"##_COMMENT1": "SAMPLE NAME AND UNMAPPED BAMS",
"PreProcessingForVariantDiscovery_GATK4.sample_name": "NA12878",
"PreProcessingForVariantDiscovery_GATK4.ref_name": "b37",
"PreProcessingForVariantDiscovery_GATK4.flowcell_unmapped_bams_list": "gs://gatk-test-data/wgs_ubam/NA12878_24RG/NA12878_24RG_small.txt",
"PreProcessingForVariantDiscovery_GATK4.unmapped_bam_suffix": ".bam",
"##_COMMENT2": "REFERENCE FILES",
"PreProcessingForVariantDiscovery_GATK4.ref_dict": "gs://gatk-legacy-bundles/b37/human_g1k_v37_decoy.dict",
"PreProcessingForVariantDiscovery_GATK4.ref_fasta": "gs://gatk-legacy-bundles/b37/human_g1k_v37_decoy.fasta",
"PreProcessingForVariantDiscovery_GATK4.ref_fasta_index": "gs://gatk-legacy-bundles/b37/human_g1k_v37_decoy.fasta.fai",
"PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.ref_sa": "gs://gatk-legacy-bundles/b37/human_g1k_v37_decoy.fasta.sa",
"PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.ref_amb": "gs://gatk-legacy-bundles/b37/human_g1k_v37_decoy.fasta.amb",
"PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.ref_bwt": "gs://gatk-legacy-bundles/b37/human_g1k_v37_decoy.fasta.bwt",
"PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.ref_ann": "gs://gatk-legacy-bundles/b37/human_g1k_v37_decoy.fasta.ann",
"PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.ref_pac": "gs://gatk-legacy-bundles/b37/human_g1k_v37_decoy.fasta.pac",
"##_COMMENT3": "KNOWN SITES RESOURCES",
"PreProcessingForVariantDiscovery_GATK4.dbSNP_vcf": "gs://gatk-legacy-bundles/b37/dbsnp_138.b37.vcf",
"PreProcessingForVariantDiscovery_GATK4.dbSNP_vcf_index": "gs://gatk-legacy-bundles/b37/dbsnp_138.b37.vcf.idx",
"PreProcessingForVariantDiscovery_GATK4.known_indels_sites_VCFs": [
"gs://gatk-legacy-bundles/b37/Mills_and_1000G_gold_standard.indels.b37.vcf"
],
"PreProcessingForVariantDiscovery_GATK4.known_indels_sites_indices": [
"gs://gatk-legacy-bundles/b37/Mills_and_1000G_gold_standard.indels.b37.vcf.idx"
],
"##_COMMENT4": "MISC PROGRAM PARAMETERS",
"#PreProcessingForVariantDiscovery_GATK4.bwa_commandline_override": "String? (optional)",
"PreProcessingForVariantDiscovery_GATK4.compression_level": 5,
"PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.num_cpu": "16",
"##_COMMENT5": "DOCKERS",
"#PreProcessingForVariantDiscovery_GATK4.gotc_docker_override": "String? (optional)",
"#PreProcessingForVariantDiscovery_GATK4.gatk_docker_override": "String? (optional)",
"#PreProcessingForVariantDiscovery_GATK4.python_docker_override": "String? (optional)",
"##_COMMENT6": "PATHS",
"#PreProcessingForVariantDiscovery_GATK4.gotc_path_override": "String? (optional)",
"#PreProcessingForVariantDiscovery_GATK4.gatk_path_override": "String? (optional)",
"##_COMMENT7": "JAVA OPTIONS",
"PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.java_opt": "-Xms3000m",
"PreProcessingForVariantDiscovery_GATK4.MergeBamAlignment.java_opt": "-Xms3000m",
"PreProcessingForVariantDiscovery_GATK4.MarkDuplicates.java_opt": "-Xms4000m",
"PreProcessingForVariantDiscovery_GATK4.SortAndFixTags.java_opt_sort": "-Xms4000m",
"PreProcessingForVariantDiscovery_GATK4.SortAndFixTags.java_opt_fix": "-Xms500m",
"PreProcessingForVariantDiscovery_GATK4.BaseRecalibrator.java_opt": "-Xms4000m",
"PreProcessingForVariantDiscovery_GATK4.GatherBqsrReports.java_opt": "-Xms3000m",
"PreProcessingForVariantDiscovery_GATK4.ApplyBQSR.java_opt": "-Xms3000m",
"PreProcessingForVariantDiscovery_GATK4.GatherBamFiles.java_opt": "-Xms2000m",
"##_COMMENT8": "MEMORY ALLOCATION",
"PreProcessingForVariantDiscovery_GATK4.GetBwaVersion.mem_size": "1 GB",
"PreProcessingForVariantDiscovery_GATK4.SamToFastqAndBwaMem.mem_size": "14 GB",
"PreProcessingForVariantDiscovery_GATK4.MergeBamAlignment.mem_size": "3500 MB",
"PreProcessingForVariantDiscovery_GATK4.MarkDuplicates.mem_size": "7 GB",
"PreProcessingForVariantDiscovery_GATK4.SortAndFixTags.mem_size": "5000 MB",
"PreProcessingForVariantDiscovery_GATK4.CreateSequenceGroupingTSV.mem_size": "2 GB",
"PreProcessingForVariantDiscovery_GATK4.BaseRecalibrator.mem_size": "6 GB",
"PreProcessingForVariantDiscovery_GATK4.GatherBqsrReports.mem_size": "3500 MB",
"PreProcessingForVariantDiscovery_GATK4.ApplyBQSR.mem_size": "3500 MB",
"PreProcessingForVariantDiscovery_GATK4.GatherBamFiles.mem_size": "3 GB",
"##_COMMENT9": "DISK SIZE ALLOCATION",
"PreProcessingForVariantDiscovery_GATK4.agg_small_disk": 200,
"PreProcessingForVariantDiscovery_GATK4.agg_medium_disk": 300,
"PreProcessingForVariantDiscovery_GATK4.agg_large_disk": 400,
"PreProcessingForVariantDiscovery_GATK4.flowcell_small_disk": 100,
"PreProcessingForVariantDiscovery_GATK4.flowcell_medium_disk": 200,
"##_COMMENT10": "PREEMPTIBLES",
"#PreProcessingForVariantDiscovery_GATK4.preemptible_tries_override": "Int? (optional)"
}