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WholeGenomeGermlineSingleSample.inputs.json
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WholeGenomeGermlineSingleSample.inputs.json
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{
"WholeGenomeGermlineSingleSample.sample_and_unmapped_bams": {
"sample_name": "NA12878",
"base_file_name": "NA1278",
"flowcell_unmapped_bams": [
"gs://gatk-test-data/wgs_ubam/NA12878_24RG/small/HJYFJ.4.NA12878.downsampled.query.sorted.unmapped.bam",
"gs://gatk-test-data/wgs_ubam/NA12878_24RG/small/HJYFJ.5.NA12878.downsampled.query.sorted.unmapped.bam",
"gs://gatk-test-data/wgs_ubam/NA12878_24RG/small/HJYFJ.6.NA12878.downsampled.query.sorted.unmapped.bam",
"gs://gatk-test-data/wgs_ubam/NA12878_24RG/small/HJYFJ.7.NA12878.downsampled.query.sorted.unmapped.bam",
"gs://gatk-test-data/wgs_ubam/NA12878_24RG/small/HJYFJ.8.NA12878.downsampled.query.sorted.unmapped.bam",
"gs://gatk-test-data/wgs_ubam/NA12878_24RG/small/HJYN2.1.NA12878.downsampled.query.sorted.unmapped.bam",
"gs://gatk-test-data/wgs_ubam/NA12878_24RG/small/HK35M.1.NA12878.downsampled.query.sorted.unmapped.bam",
"gs://gatk-test-data/wgs_ubam/NA12878_24RG/small/HK35M.2.NA12878.downsampled.query.sorted.unmapped.bam",
"gs://gatk-test-data/wgs_ubam/NA12878_24RG/small/HK35M.3.NA12878.interval.filtered.query.sorted.unmapped.bam",
"gs://gatk-test-data/wgs_ubam/NA12878_24RG/small/HK35M.4.NA12878.interval.filtered.query.sorted.unmapped.bam",
"gs://gatk-test-data/wgs_ubam/NA12878_24RG/small/HK35M.5.NA12878.interval.filtered.query.sorted.unmapped.bam",
"gs://gatk-test-data/wgs_ubam/NA12878_24RG/small/HK35M.6.NA12878.interval.filtered.query.sorted.unmapped.bam",
"gs://gatk-test-data/wgs_ubam/NA12878_24RG/small/HK35M.7.NA12878.interval.filtered.query.sorted.unmapped.bam",
"gs://gatk-test-data/wgs_ubam/NA12878_24RG/small/HK35M.8.NA12878.interval.filtered.query.sorted.unmapped.bam",
"gs://gatk-test-data/wgs_ubam/NA12878_24RG/small/HK35N.1.NA12878.interval.filtered.query.sorted.unmapped.bam",
"gs://gatk-test-data/wgs_ubam/NA12878_24RG/small/HK35N.2.NA12878.interval.filtered.query.sorted.unmapped.bam",
"gs://gatk-test-data/wgs_ubam/NA12878_24RG/small/HK3T5.1.NA12878.interval.filtered.query.sorted.unmapped.bam",
"gs://gatk-test-data/wgs_ubam/NA12878_24RG/small/HK3T5.2.NA12878.interval.filtered.query.sorted.unmapped.bam",
"gs://gatk-test-data/wgs_ubam/NA12878_24RG/small/HK3T5.3.NA12878.interval.filtered.query.sorted.unmapped.bam",
"gs://gatk-test-data/wgs_ubam/NA12878_24RG/small/HK3T5.4.NA12878.interval.filtered.query.sorted.unmapped.bam",
"gs://gatk-test-data/wgs_ubam/NA12878_24RG/small/HK3T5.5.NA12878.interval.filtered.query.sorted.unmapped.bam",
"gs://gatk-test-data/wgs_ubam/NA12878_24RG/small/HK3T5.6.NA12878.interval.filtered.query.sorted.unmapped.bam",
"gs://gatk-test-data/wgs_ubam/NA12878_24RG/small/HK3T5.7.NA12878.interval.filtered.query.sorted.unmapped.bam",
"gs://gatk-test-data/wgs_ubam/NA12878_24RG/small/HK3T5.8.NA12878.interval.filtered.query.sorted.unmapped.bam"
],
"final_gvcf_base_name": "NA12878",
"unmapped_bam_suffix": ".bam"
},
"WholeGenomeGermlineSingleSample.references": {
"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",
"calling_interval_list": "gs://gcp-public-data--broad-references/hg38/v0/wgs_calling_regions.hg38.interval_list",
"reference_fasta": {
"ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
"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_alt": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.alt",
"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_ann": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.64.ann",
"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"
],
"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",
"evaluation_interval_list": "gs://gcp-public-data--broad-references/hg38/v0/wgs_evaluation_regions.hg38.interval_list",
"haplotype_database_file": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.haplotype_database.txt"
},
"WholeGenomeGermlineSingleSample.scatter_settings": {
"haplotype_scatter_count": 50,
"break_bands_at_multiples_of": 1000000
},
"WholeGenomeGermlineSingleSample.fingerprint_genotypes_file": "gs://dsde-data-na12878-public/NA12878.hg38.reference.fingerprint.vcf",
"WholeGenomeGermlineSingleSample.wgs_coverage_interval_list": "gs://gcp-public-data--broad-references/hg38/v0/wgs_coverage_regions.hg38.interval_list",
"WholeGenomeGermlineSingleSample.papi_settings": {
"preemptible_tries": 3,
"agg_preemptible_tries": 3
}
}