variant-calling/defaults

{
  "tumor_fastq_1": "",
  "tumor_fastq_2": "",
  "normal_fastq_1": "",
  "normal_fastq_2": "",
  "tumor_deduped_bam": "",
  "normal_deduped_bam": "",
  "pl": "ILLUMINAL",
  "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",
  "hg": "hg38",
  "annovar_database": "oss://pgx-reference-data/annovar/",
  "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",
  "regions": "oss://pgx-reference-data/bed/cbcga/S07604514_Padded.bed",
  "interval_padding": "0",
  "sentieon_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v202010.02",
  "varscan_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/varscan2:v2.4.3",
  "pindel_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/pindel:0.2.5b9_3",
  "samtools_docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/samtools:v1.3.1",
  "annovar_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/annovar:v2019.10",
  "vep_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/vep:v104.0",
  "cache": "oss://pgx-reference-data/ensembl_vep/",
  "vep_path": "/opt/vep/ensembl-vep",
  "species": "homo_sapiens_merged",
  "vcf2maf_path": "/opt/mskcc-vcf2maf",
  "tnseq_pon": "",
  "tnscope_pon": "",
  "disk_size": "200",
  "cluster_config": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc",
  "haplotyper": false,
  "pindel": false,
  "tnseq": false,
  "tnscope": false,
  "varscan": false,
  "annovar": false,
  "vep": false,
  "only_pass": true,
  "input_fastq": false,
  "input_bam": false
}