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beagle-refine-impute.json
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beagle-refine-impute.json
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{
"##_COMMENT0": "INPUT/OUTPUT VCF",
"LowCovImputation.input_vcf": "gs://neurogap/high_coverage/neurogap_4.0X.vcf.gz",
"LowCovImputation.refined_base": "gs://neurogap/high_coverage/neurogap_4.0X.refined",
"LowCovImputation.imputed_base": "gs://neurogap/high_coverage/neurogap_4.0X.imputed",
"##_COMMENT1": "REFERENCE FILES",
"#LowCovImputation.reference_refine": "gs://neurogap/reference_data/AFR.chr15.shapeit2_integrated_v1a.GRCh38.20181129.phased.vcf.gz",
"#LowCovImputation.reference_impute": "gs://neurogap/reference_data/ALL.chr15.shapeit2_integrated_v1a.GRCh38.20181129.phased.vcf.gz",
"#LowCovImputation.recomb_map": "gs://neurogap/reference_data/plink.chr14.GRCh38.map",
"LowCovImputation.ref_file": "gs://neurogap/reference_data/ref_files.txt",
"##_COMMENT2": "TO REFINE OR NOT TO REFINE",
"LowCovImputation.run_refine_genotypes": "true",
"LowCovImputation.run_impute_genotypes": "true",
"##_COMMENT3": "INTERVALS",
"LowCovImputation.intervals_file": "gs://neurogap/reference_data/hg38_wgs_refine_intervals_5mb_overlapping.txt",
"LowCovImputation.intervals_chrom": "gs://neurogap/reference_data/hg38_wgs_refine_intervals.txt",
"LowCovImputation.eval_interval_list": "gs://broad-references/hg38/v0/wgs_evaluation_regions.hg38.interval_list",
"##_COMMENT4": "RESOURCE FILES",
"LowCovImputation.ref_fasta": "gs://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
"LowCovImputation.ref_fasta_index": "gs://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
"LowCovImputation.ref_dict": "gs://broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
"LowCovImputation.dbsnp_vcf": "gs://broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf",
"LowCovImputation.dbsnp_vcf_index": "gs://broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf.idx",
"##_COMMENT5": "DOCKERS",
"#LowCovImputation.beagle_docker_override": "String? (optional)",
"#LowCovImputation.gatk_docker_override": "String? (optional)",
"#LowCovImputation.gitc_docker_override": "String? (optional)",
"##_COMMENT6": "PATHS",
"#LowCovImputation.gatk_path_override": "String? (optional)",
"#LowCovImputation.samtools_path_override": "String? (optional)",
"##_COMMENT7": "JAVA OPTIONS",
"#LowCovImputation.HaplotypeCaller.java_options": "String? (optional)",
"##_COMMENT8": "MEMORY ALLOCATION",
"#LowCovImputation.HaplotypeCaller.mem_gb": "Int? (optional)",
"#LowCovImputation.MergeGVCFs.mem_gb": "Int? (optional)",
"#LowCovImputation.CramToBamTask.machine_mem_gb": "Int? (optional)",
"##_COMMENT9": "DISK SIZE ALLOCATION",
"#LowCovImputation.HaplotypeCaller.disk_space_gb": "Int? (optional)",
"#LowCovImputation.MergeGVCFs.disk_space_gb": "Int? (optional)",
"#LowCovImputation.CramToBamTask.disk_space_gb": 300,
"##_COMMENT10": "PREEMPTION",
"#LowCovImputation.HaplotypeCaller.preemptible_attempts": "Int? (optional)",
"#LowCovImputation.MergeGVCFs.preemptible_attempts": "Int? (optional)",
"#LowCovImputation.CramToBamTask.preemptible_attempts": 4
}