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Copy pathWholeGenomeGermlineSingleSample.local.json
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WholeGenomeGermlineSingleSample.local.json
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{
"WholeGenomeGermlineSingleSample.sample_and_unmapped_bams": {
"sample_name": "GGSpi001",
"base_file_name": "GGSpi001",
"flowcell_unmapped_bams": ["/data/og/GGSpi/output/GGSpi001_FKDN20H102299-1A_HHHJNDSXY_L1.unmapped.bam","/data/og/GGSpi/output/GGSpi001_FKDN20H102299-1A_HF7HFDSXY_L2.unmapped.bam"],
"final_gvcf_base_name": "GGSpi001",
"unmapped_bam_suffix": ".unmapped.bam"
},
"WholeGenomeGermlineSingleSample.references": {
"contamination_sites_ud": "/data/og/reference_files/Homo_sapiens_assembly38.contam.UD",
"contamination_sites_bed": "/data/og/reference_files/Homo_sapiens_assembly38.contam.bed",
"contamination_sites_mu": "/data/og/reference_files/Homo_sapiens_assembly38.contam.mu",
"calling_interval_list": "/data/og/reference_files/wgs_calling_regions.hg38.interval_list",
"reference_fasta": {
"ref_dict": "/data/og/reference_files/Homo_sapiens_assembly38.dict",
"ref_fasta": "/data/og/reference_files/Homo_sapiens_assembly38.fasta",
"ref_fasta_index": "/data/og/reference_files/Homo_sapiens_assembly38.fasta.fai",
"ref_alt": "/data/og/reference_files/Homo_sapiens_assembly38.fasta.64.alt",
"ref_sa": "/data/og/reference_files/Homo_sapiens_assembly38.fasta.64.sa",
"ref_amb": "/data/og/reference_files/Homo_sapiens_assembly38.fasta.64.amb",
"ref_bwt": "/data/og/reference_files/Homo_sapiens_assembly38.fasta.64.bwt",
"ref_ann": "/data/og/reference_files/Homo_sapiens_assembly38.fasta.64.ann",
"ref_pac": "/data/og/reference_files/Homo_sapiens_assembly38.fasta.64.pac"
},
"known_indels_sites_vcfs": [
"/data/og/reference_files/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
"/data/og/reference_files/Homo_sapiens_assembly38.known_indels.vcf.gz"
],
"known_indels_sites_indices": [
"/data/og/reference_files/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi",
"/data/og/reference_files/Homo_sapiens_assembly38.known_indels.vcf.gz.tbi"
],
"dbsnp_vcf": "/data/og/reference_files/Homo_sapiens_assembly38.dbsnp138.vcf",
"dbsnp_vcf_index": "/data/og/reference_files/Homo_sapiens_assembly38.dbsnp138.vcf.idx",
"evaluation_interval_list": "/data/og/reference_files/wgs_evaluation_regions.hg38.interval_list",
"haplotype_database_file": "/data/og/reference_files/Homo_sapiens_assembly38.haplotype_database.txt"
},
"WholeGenomeGermlineSingleSample.scatter_settings": {
"haplotype_scatter_count": 50,
"break_bands_at_multiples_of": 1000000
},
"WholeGenomeGermlineSingleSample.wgs_coverage_interval_list": "/data/og/reference_files/wgs_coverage_regions.hg38.interval_list",
"WholeGenomeGermlineSingleSample.papi_settings": {
"preemptible_tries": 3,
"agg_preemptible_tries": 3
},
"WholeGenomeGermlineSingleSample.provide_bam_output": true,
"WholeGenomeGermlineSingleSample.use_gatk3_haplotype_caller": false,
"WholeGenomeGermlineSingleSample.UnmappedBamToAlignedBam.output_sorted_bam": true,
"WholeGenomeGermlineSingleSample.UnmappedBamToAlignedBam.cpu": 4
}