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quartet_dna_quality_control_wes_big_pipeline
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  1. {

  2.   "benchmarking_dir": "oss://pgx-result/renluyao/manuscript_v3.0/reference_datasets_v202103/",

  3.   "SENTIEON_INSTALL_DIR": "/opt/sentieon-genomics",

  4.   "fasta": "GRCh38.d1.vd1.fa",

  5.   "BENCHMARKdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-hap:latest",

  6.   "dbsnp_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",

  7.   "BEDTOOLSdocker": "registry-internal.cn-shanghai.aliyuncs.com/pgx-docker-registry/bedtools:v2.27.1",

  8.   "PICARDdocker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/picard:2.25.4",

  9.   "disk_size": "500",

  10.   "reference_bed_dict": "oss://pgx-reference-data/GRCh38.d1.vd1/GRCh38.d1.vd1.dict",

  11.   "FASTQCdocker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqc:0.11.8",

  12.   "MULTIQCdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/multiqc:v1.8",

  13.   "SMALLcluster_config": "OnDemand bcs.ps.g.xlarge img-ubuntu-vpc",

  14.   "screen_ref_dir": "oss://pgx-reference-data/fastq_screen_reference/",

  15.   "fastq_1_D5": "",

  16.   "dbmills_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",

  17.   "BIGcluster_config": "OnDemand bcs.a2.7xlarge img-ubuntu-vpc",

  18.   "fastq_screen_conf": "oss://pgx-reference-data/fastq_screen_reference/fastq_screen.conf",

  19.   "FASTQSCREENdocker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqscreen:0.12.0",

  20.   "SENTIEON_LICENSE": "192.168.0.55:8990",

  21.   "SENTIEONdocker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2019.11.28",

  22.   "QUALIMAPdocker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/qualimap:2.0.0",

  23.   "vcf_D5": "",

  24.   "benchmark_region": "oss://pgx-result/renluyao/manuscript_v3.0/reference_datasets_v202103/Quartet.high.confidence.region.v202103.bed",

  25.   "db_mills": "Mills_and_1000G_gold_standard.indels.hg38.vcf",

  26.   "dbsnp": "dbsnp_146.hg38.vcf",

  27.   "MENDELIANdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/vbt:v1.1",

  28.   "DIYdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/high_confidence_call_manuscript:v1.4",

  29.   "ref_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/"

  30. }