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variant-calling
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Germline & Somatic short variant discovery (SNVs + Indels) for WGS & WES.
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variant-calling/defaults

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  1. {

  2.   "tumor_fastq_1": "",

  3.   "tumor_fastq_2": "",

  4.   "normal_fastq_1": "",

  5.   "normal_fastq_2": "",

  6.   "tumor_deduped_bam": "",

  7.   "tumor_deduped_bam_index": "",

  8.   "normal_deduped_bam": "",

  9.   "normal_deduped_bam_index": "",

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

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

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

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

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

  15.   "SENTIEON_LICENSE": "192.168.0.55:8990",

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

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

  18.   "hg": "hg38",

  19.   "annovar_database": "oss://pgx-reference-data/annovar/",

  20.   "germline_resource": "oss://pgx-reference-data/gnomAD/af-only-gnomad.v3.1.1.vcf.gz",

  21.   "germline_resource_tbi": "oss://pgx-reference-data/gnomAD/af-only-gnomad.v3.1.1.vcf.gz.tbi",

  22.   "regions": "oss://pgx-reference-data/bed/cbcga/S07604514_Padded.bed",

  23.   "interval_padding": "0",

  24.   "sentieon_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v202010.02",

  25.   "varscan_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/varscan2:v2.4.3",

  26.   "annovar_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/annovar:v2019.10",

  27.   "vep_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/vep:v104.0",

  28.   "cache": "oss://pgx-reference-data/ensembl_vep/",

  29.   "vep_path": "/opt/vep/ensembl-vep",

  30.   "species": "homo_sapiens_merged",

  31.   "vcf2maf_path": "/opt/mskcc-vcf2maf",

  32.   "tnseq_pon": "",

  33.   "tnscope_pon": "",

  34.   "disk_size": "200",

  35.   "cluster_config": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc",

  36.   "haplotyper": false,

  37.   "tnseq": false,

  38.   "tnscope": false,

  39.   "varscan": false,

  40.   "annovar": false,

  41.   "vep": false,

  42.   "only_pass": true

  43. }