This repository has been archived by the owner on Jan 25, 2020. It is now read-only.
-
Notifications
You must be signed in to change notification settings - Fork 44
/
WholeGenomeGermlineSingleSample.hg38.inputs.json
53 lines (50 loc) · 3.44 KB
/
WholeGenomeGermlineSingleSample.hg38.inputs.json
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
{
"WholeGenomeGermlineSingleSample.sample_and_unmapped_bams": {
"sample_name": "NA12878 PLUMBING",
"base_file_name": "NA12878_PLUMBING",
"flowcell_unmapped_bams": [
"gs://broad-public-datasets/NA12878_downsampled_for_testing/unmapped/H06HDADXX130110.1.ATCACGAT.20k_reads.bam",
"gs://broad-public-datasets/NA12878_downsampled_for_testing/unmapped/H06HDADXX130110.2.ATCACGAT.20k_reads.bam",
"gs://broad-public-datasets/NA12878_downsampled_for_testing/unmapped/H06JUADXX130110.1.ATCACGAT.20k_reads.bam"
],
"final_gvcf_base_name": "NA12878_PLUMBING",
"unmapped_bam_suffix": ".bam"
},
"WholeGenomeGermlineSingleSample.references": {
"fingerprint_genotypes_file": "gs://dsde-data-na12878-public/NA12878.hg38.reference.fingerprint.vcf",
"fingerprint_genotypes_index": "gs://dsde-data-na12878-public/NA12878.hg38.reference.fingerprint.vcf.idx",
"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",
"haplotype_scatter_count": 10,
"break_bands_at_multiples_of": 100000,
"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"
},
"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
}
}