YaqingLiu
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CNVkit-test
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CNVkit-test/defaults

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  1. {

  2.   "tumor_bam": "",

  3.   "tumor_bam_index": "",

  4.   "normal_bam": "",

  5.   "normal_bam_index": "",

  6.   "read_structure": "",

  7.   "duplex_umi": "",

  8.   "platform": "MGI",

  9.   "regions": "oss://ivd-product/reference/bed/Dynegene/SureSelectXT_HS_V8_S33266340_hg38_Regions.bed",

  10.   "interval_padding": "0",

  11.   "SENTIEON_LICENSE": "172.25.164.226:8990",

  12.   "fasta": "GRCh38_full_analysis_set_plus_decoy_hla.fa",

  13.   "ref_dir": "oss://ivd-product/reference/refGenome/",

  14.   "ref_flat": "oss://ivd-product/reference/refGenome/refFlat.hg38.txt",

  15.   "dbmills_dir": "oss://genomics-platform-reference-data/GRCh38.d1.vd1/",

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

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

  18.   "dbsnp_dir": "oss://genomics-platform-reference-data/GRCh38.d1.vd1/",

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

  20.   "annotsv_database": "oss://ivd-product/reference/AnnotSV/",

  21.   "germline_resource": "oss://genomics-platform-reference-data/gnomAD/af-only-gnomad.v3.1.1.vcf.gz",

  22.   "germline_resource_tbi": "oss://genomics-platform-reference-data/gnomAD/af-only-gnomad.v3.1.1.vcf.gz.tbi",

  23.   "gc": "oss://ivd-product/reference/Sequenza/GRCh38.gc50Base.wig.gz",

  24.   "baseline": "oss://ivd-product/reference/MSIsensor/hg38_reference.list_baseline",

  25.   "sentieon_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/sentieon-genomics:v202112.05",

  26.   "manta_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/manta:1.6.0",

  27.   "bcftools_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/bcftools:v1.9",

  28.   "annovar_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/annovar:v20191024",

  29.   "annotsv_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/annotsv:3.1.3",

  30.   "cnvkit_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/cnvkit:0.9.9",

  31.   "sequenza_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/sequenza:3.0.0",

  32.   "msisensor_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/msisensor-pro:1.2.0",

  33.   "tmb_docker": "registry.cn-shanghai.aliyuncs.com/choppy-pipe/tmb:1.0.0",

  34.   "cluster_config": "OnDemand bcs.es.c.large img-ubuntu-vpc",

  35.   "disk_size": "200"

  36. }