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@bshifaw bshifaw Dev (#31) 63c7ac0 Feb 28, 2019
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@bshifaw @ruchim
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{
"##_COMMENT1": "INPUT GVCFs & COHORT -- DATASET-SPECIFC, MUST BE ADAPTED",
"JointGenotyping.callset_name": "NA12878",
"JointGenotyping.sample_name_map": "gs://gatk-test-data/joint_discovery/NA12878.sample_map",
"##_COMMENT2": "REFERENCE FILES",
"JointGenotyping.ref_fasta": "gs://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
"JointGenotyping.ref_fasta_index": "gs://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
"JointGenotyping.ref_dict": "gs://broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
"##_COMMENT3": "INTERVALS",
"JointGenotyping.eval_interval_list": "gs://broad-references/hg38/v0/wgs_evaluation_regions.hg38.interval_list",
"JointGenotyping.unpadded_intervals_file": "gs://gatk-test-data/intervals/hg38.even.handcurated.20k.intervals",
"##_COMMENT4": "RESOURCE FILES",
"JointGenotyping.dbsnp_vcf": "gs://broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf",
"JointGenotyping.dbsnp_vcf_index": "gs://broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf.idx",
"JointGenotyping.one_thousand_genomes_resource_vcf": "gs://broad-references/hg38/v0/1000G_phase1.snps.high_confidence.hg38.vcf.gz",
"JointGenotyping.one_thousand_genomes_resource_vcf_index": "gs://broad-references/hg38/v0/1000G_phase1.snps.high_confidence.hg38.vcf.gz.tbi",
"JointGenotyping.omni_resource_vcf": "gs://broad-references/hg38/v0/1000G_omni2.5.hg38.vcf.gz",
"JointGenotyping.omni_resource_vcf_index": "gs://broad-references/hg38/v0/1000G_omni2.5.hg38.vcf.gz.tbi",
"JointGenotyping.mills_resource_vcf": "gs://broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
"JointGenotyping.mills_resource_vcf_index": "gs://broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi",
"JointGenotyping.axiomPoly_resource_vcf": "gs://broad-references/hg38/v0/Axiom_Exome_Plus.genotypes.all_populations.poly.hg38.vcf.gz",
"JointGenotyping.axiomPoly_resource_vcf_index": "gs://broad-references/hg38/v0/Axiom_Exome_Plus.genotypes.all_populations.poly.hg38.vcf.gz.tbi",
"JointGenotyping.hapmap_resource_vcf": "gs://broad-references/hg38/v0/hapmap_3.3.hg38.vcf.gz",
"JointGenotyping.hapmap_resource_vcf_index": "gs://broad-references/hg38/v0/hapmap_3.3.hg38.vcf.gz.tbi",
"##_COMMENT5": "VQSR PARAMETERS",
"JointGenotyping.SNP_VQSR_downsampleFactor": 10,
"JointGenotyping.snp_filter_level": 99.7,
"JointGenotyping.indel_filter_level": 99.7,
"JointGenotyping.indel_recalibration_annotation_values": ["FS", "ReadPosRankSum", "MQRankSum", "QD", "SOR", "DP"],
"JointGenotyping.indel_recalibration_tranche_values": ["100.0", "99.95", "99.9", "99.5", "99.0", "97.0", "96.0", "95.0", "94.0", "93.5", "93.0", "92.0", "91.0", "90.0"],
"JointGenotyping.snp_recalibration_tranche_values": ["100.0", "99.95", "99.9", "99.8", "99.6", "99.5", "99.4", "99.3", "99.0", "98.0", "97.0", "90.0" ],
"JointGenotyping.snp_recalibration_annotation_values": ["QD", "MQRankSum", "ReadPosRankSum", "FS", "MQ", "SOR", "DP"],
"##_COMMENT4": "DOCKERS",
"#PreProcessingForVariantDiscovery_GATK4.gatk_docker_override": "String? (optional)",
"##_COMMENT5": "PATHS",
"#PreProcessingForVariantDiscovery_GATK4.gatk_path_override": "String? (optional)",
"##_COMMENT6": "JAVA OPTIONS",
"JointGenotyping.SNPsVariantRecalibratorScattered.java_opt": "-Xmx3g -Xms3g",
"JointGenotyping.CollectMetricsOnFullVcf.java_opt": "-Xmx6g -Xms6g",
"JointGenotyping.IndelsVariantRecalibrator.java_opt": "-Xmx24g -Xms24g",
"JointGenotyping.HardFilterAndMakeSitesOnlyVcf.java_opt": "-Xmx3g -Xms3g",
"JointGenotyping.SNPGatherTranches.java_opt": "-Xmx6g -Xms6g",
"JointGenotyping.CollectMetricsSharded.java_opt": "-Xmx6g -Xms6g",
"JointGenotyping.SitesOnlyGatherVcf.java_opt": "-Xmx6g -Xms6g",
"JointGenotyping.ApplyRecalibration.java_opt": "-Xmx5g -Xms5g",
"JointGenotyping.FinalGatherVcf.java_opt": "-Xmx6g -Xms6g",
"JointGenotyping.ImportGVCFs.java_opt": "-Xmx4g -Xms4g",
"JointGenotyping.SNPsVariantRecalibratorCreateModel.java_opt": "-Xmx100g -Xms100g",
"JointGenotyping.GatherMetrics.java_opt": "-Xmx2g -Xms2g",
"JointGenotyping.GenotypeGVCFs.java_opt": "-Xmx5g -Xms5g",
"##_COMMENT7": "MEMORY ALLOCATION",
"JointGenotyping.CollectMetricsSharded.mem_size": "7 GB",
"JointGenotyping.ImportGVCFs.mem_size": "7 GB",
"JointGenotyping.IndelsVariantRecalibrator.mem_size": "26 GB",
"JointGenotyping.ApplyRecalibration.mem_size": "7 GB",
"JointGenotyping.CollectMetricsOnFullVcf.mem_size": "7 GB",
"JointGenotyping.GenotypeGVCFs.mem_size": "7 GB",
"JointGenotyping.FinalGatherVcf.mem_size": "7 GB",
"JointGenotyping.SitesOnlyGatherVcf.mem_size": "7 GB",
"JointGenotyping.SNPsVariantRecalibratorScattered.mem_size": "3.5 GB",
"JointGenotyping.SNPsVariantRecalibratorCreateModel.mem_size": "104 GB",
"JointGenotyping.DynamicallyCombineIntervals.mem_size": "3 GB",
"JointGenotyping.GatherMetrics.mem_size": "3 GB",
"JointGenotyping.HardFilterAndMakeSitesOnlyVcf.mem_size": "3.5 GB",
"JointGenotyping.SNPGatherTranches.mem_size": "7 GB",
"##_COMMENT8": "DISK SIZE ALLOCATION",
"#JointGenotyping.small_disk_override": "Int? (optional)",
"#JointGenotyping.medium_disk_override": "Int? (optional)",
"#JointGenotyping.large_disk_override": "Int? (optional)",
"#JointGenotyping.huge_disk_override": "Int? (optional)",
"##_COMMENT9": "PREEMPTIBLES",
"#PreProcessingForVariantDiscovery_GATK4.preemptible_tries_override": "Int? (optional)"
}
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