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RNAseq_Variant_Calling
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从RNAseq数据中call突变
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RNAseq_Variant_Calling/inputs

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  1. {

  2.   "{{ project_name }}.indexBam.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/samtools:v1.3.1",

  3.   "{{ project_name }}.Haplotyper.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2018.08.01",

  4.   "{{ project_name }}.SENTIEON_INSTALL_DIR": "/opt/sentieon-genomics",

  5.   "{{ project_name }}.fasta": "GRCh38.d1.vd1.fa",

  6.   "{{ project_name }}.Dedup.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2018.08.01",

  7.   "{{ project_name }}.dbsnp_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",

  8.   "{{ project_name }}.deduped_Metrics.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2018.08.01",

  9.   "{{ project_name }}.disk_size": "500",

  10.   "{{ project_name }}.fastq_1": "{{ fastq_1 }}",

  11.   "{{ project_name }}.Metrics.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2018.08.01",

  12.   "{{ project_name }}.STARref_dir": "oss://chinese-quartet/quartet-storage-data/reference_data/STAR_GRCh38_2.7.0d/",

  13.   "{{ project_name }}.fastq_2": "{{ fastq_2 }}",

  14.   "{{ project_name }}.dbmills_dir": "oss://pgx-reference-data/GRCh38.d1.vd1/",

  15.   "{{ project_name }}.SplitReads.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2018.08.01",

  16.   "{{ project_name }}.cluster_config": "OnDemand bcs.ps.g.8xlarge img-ubuntu-vpc",

  17.   "{{ project_name }}.Hardfiltration.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/gatk:v2019.01",

  18.   "{{ project_name }}.BQSR.docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/sentieon-genomics:v2018.08.01",

  19.   "{{ project_name }}.mapping.docker": "registry-vpc.cn-shanghai.aliyuncs.com/pgx-docker-registry/star:2.7.0",

  20.   "{{ project_name }}.db_mills": "Mills_and_1000G_gold_standard.indels.hg38.vcf",

  21.   "{{ project_name }}.sample": "{{ sample }}",

  22.   "{{ project_name }}.dbsnp": "dbsnp_146.hg38.vcf",

  23.   "{{ project_name }}.ref_dir": "oss://chinese-quartet/quartet-storage-data/reference_data/"

  24. }