quartet_dna_quality_control_wes_big_pipeline/defaults

{
  "benchmarking_dir": "oss://pgx-result/renluyao/manuscript_v3.0/reference_datasets_v202103/",
  "fasta": "GRCh38.d1.vd1.fa",
  "BENCHMARKdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/rtg-hap:latest",
  "dbsnp_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
  "BEDTOOLSdocker": "registry-internal.cn-shanghai.aliyuncs.com/pgx-docker-registry/bedtools:v2.27.1",
  "PICARDdocker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/picard:2.25.4",
  "disk_size": "500",
  "reference_bed_dict": "oss://pgx-reference-data/GRCh38.d1.vd1/GRCh38.d1.vd1.dict",
  "FASTQCdocker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqc:0.11.8",
  "MULTIQCdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/multiqc:v1.8",
  "SMALLcluster_config": "OnDemand bcs.ps.g.xlarge img-ubuntu-vpc",
  "screen_ref_dir": "oss://pgx-reference-data/fastq_screen_reference/",
  "fastq_1_D5": "",
  "dbmills_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
  "BIGcluster_config": "OnDemand bcs.a2.7xlarge img-ubuntu-vpc",
  "fastq_screen_conf": "oss://pgx-reference-data/fastq_screen_reference/fastq_screen.conf",
  "FASTQSCREENdocker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqscreen:0.12.0",
  "REPLACE_SENTIEON_DOCKER": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-replaced:2.0",
  "DEEPVARIANT_DOCKER": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/deepvariant:v1.5.0_20230721",
  "QUALIMAPdocker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/qualimap:2.0.0",
  "vcf_D5": "",
  "benchmark_region": "oss://pgx-result/renluyao/manuscript_v3.0/reference_datasets_v202103/Quartet.high.confidence.region.v202103.bed",
  "db_mills": "Mills_and_1000G_gold_standard.indels.hg38.vcf",
  "dbsnp": "dbsnp_146.hg38.vcf",
  "MENDELIANdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/vbt:v1.1",
  "DIYdocker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/high_confidence_call_manuscript:1.5",
  "ref_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
  "pl": "ILLUMINA"
}