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ExomeGermlineSingleSample.inputs.json
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ExomeGermlineSingleSample.inputs.json
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{
"ExomeGermlineSingleSample.sample_and_unmapped_bams": {
"final_gvcf_base_name": "HG00133.GRCh38DH.exome",
"unmapped_bam_suffix": ".unmapped.bam",
"flowcell_unmapped_bams": ["gs://gatk-best-practices/exome-analysis-pipeline/SRR099969.unmapped.bam"],
"sample_name": "HG00133",
"base_file_name": "HG00133.GRCh38DH.exome"
},
"ExomeGermlineSingleSample.references": {
"break_bands_at_multiples_of": 1000000,
"calling_interval_list": "gs://gcp-public-data--broad-references/hg38/v0/exome_calling_regions.v1.interval_list",
"dbsnp_vcf": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf",
"dbsnp_vcf_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf.idx",
"reference_fasta": {
"ref_fasta": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
"ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
"ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
"ref_alt": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.alt",
"ref_ann": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.ann",
"ref_sa": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.sa",
"ref_amb": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.amb",
"ref_bwt": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.bwt",
"ref_pac": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.pac"
},
"known_indels_sites_vcfs": [
"gs://gcp-public-data--broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
"gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz"
],
"known_indels_sites_indices": [
"gs://gcp-public-data--broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi",
"gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz.tbi"
],
"contamination_sites_ud": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.contam.UD",
"contamination_sites_bed": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.contam.bed",
"contamination_sites_mu": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.contam.mu",
"evaluation_interval_list": "gs://gcp-public-data--broad-references/hg38/v0/exome_evaluation_regions.v1.interval_list",
"haplotype_scatter_count": 50
},
"ExomeGermlineSingleSample.target_interval_list": "gs://gcp-public-data--broad-references/hg38/v0/exome_calling_regions.v1.interval_list",
"ExomeGermlineSingleSample.bait_interval_list": "gs://gcp-public-data--broad-references/hg38/v0/exome_calling_regions.v1.interval_list",
"ExomeGermlineSingleSample.bait_set_name": "whole_exome_illumina_coding_v1",
"ExomeGermlineSingleSample.papi_settings": {
"preemptible_tries": 3,
"agg_preemptible_tries": 3
}
}