variant-calling/defaults

{
    "fasta": "GRCh38.d1.vd1.fa",
    "ref_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
    "dbsnp": "dbsnp_146.hg38.vcf",
    "dbsnp_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
    "SENTIEON_INSTALL_DIR": "/opt/sentieon-genomics",
    "SENTIEON_LICENSE": "192.168.0.55:8990",
    "dbmills_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",
    "db_mills": "Mills_and_1000G_gold_standard.indels.hg38.vcf",
    "germline_resource": "oss://pgx-reference-data/gnomAD/af-only-gnomad.v3.1.1.vcf.gz",
    "germline_resource_tbi": "oss://pgx-reference-data/gnomAD/af-only-gnomad.v3.1.1.vcf.gz.tbi",
    "sentieon_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2020.10.07",
    "varscan_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/varscan2:v2.4.3",
    "annovar_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/annovar:v2018.04",
    "maftools_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/r-base:4.0.2",
    "bcftools_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/bcftools:v1.9",
    "database": "oss://pgx-reference-data/annovar_hg38/",
    "regions": "oss://pgx-reference-data/bed/cbcga/S07604514_Covered.bed",
    "tnseq_pon": "",
    "tnscope_pon": "",
    "cosmic_vcf": "CosmicCodingMuts.hg38.v91.vcf",
    "cosmic_dir": "oss://pgx-reference-data/reference/cosmic/",
    "disk_size": "200",
    "cluster_config": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc",
    "germline": false,
    "tnseq": true,
    "tnscope": true,
    "varscan": true
}