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gatk-args.yaml
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gatk-args.yaml
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resources:
zones:
- us-*
inputs:
sample_name: NA12878
flowcell_unmapped_bams: |
gs://genomics-public-data/test-data/dna/wgs/hiseq2500/NA12878/H06HDADXX130110.1.ATCACGAT.20k_reads.bam
gs://genomics-public-data/test-data/dna/wgs/hiseq2500/NA12878/H06HDADXX130110.2.ATCACGAT.20k_reads.bam
gs://genomics-public-data/test-data/dna/wgs/hiseq2500/NA12878/H06JUADXX130110.1.ATCACGAT.20k_reads.bam
final_gvcf_name: NA12878.g.vcf.gz
agg_small_disk: 200
agg_medium_disk: 300
agg_large_disk: 400
flowcell_small_disk: 200
flowcell_medium_disk: 300
unmapped_bam_suffix: .bam
ref_dict: gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.dict
ref_fasta: gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta
ref_fasta_index: gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.fai
ref_alt: gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.64.alt
ref_bwt: gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.64.bwt
ref_sa: gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.64.sa
ref_amb: gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.64.amb
ref_ann: gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.64.ann
ref_pac: gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.64.pac
dbSNP_vcf: gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf
dbSNP_vcf_index: gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf.idx
known_snps_sites_vcf: gs://genomics-public-data/resources/broad/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
known_snps_sites_vcf_index: gs://genomics-public-data/resources/broad/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi
known_indels_sites_vcf: gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz
known_indels_sites_vcf_index: gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz.tbi
wgs_coverage_interval_list: gs://genomics-public-data/resources/broad/hg38/v0/wgs_calling_regions.hg38.interval_list
scattered_calling_intervals: |
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0001_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0002_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0003_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0004_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0005_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0006_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0007_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0008_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0009_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0010_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0011_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0012_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0013_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0014_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0015_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0016_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0017_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0018_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0019_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0020_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0021_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0022_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0023_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0024_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0025_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0026_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0027_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0028_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0029_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0030_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0031_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0032_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0033_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0034_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0035_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0036_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0037_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0038_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0039_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0040_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0041_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0042_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0043_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0044_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0045_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0046_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0047_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0048_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0049_of_50/scattered.interval_list
gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals/temp_0050_of_50/scattered.interval_list