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get_dedup_bam
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get_dedup_bam/defaults

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  1. {

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

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

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

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

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

  7.     "SENTIEON_LICENSE": "192.168.0.55:8990",

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

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

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

  11.     "database": "oss://pgx-reference-data/annovar_hg38/",

  12.     "regions": "oss://pgx-reference-data/reference/wes_bedfiles/agilent_v6/SureSelect_Human_All_Exon_V6_r2.bed",

  13.     "cosmic_vcf": "CosmicCodingMuts.hg38.v91.vcf",

  14.     "cosmic_dir": "oss://pgx-reference-data/reference/cosmic/",

  15.     "disk_size": "200",

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

  17. }