20180202_test.yaml

20180202_test.yaml

details:
- algorithm:
    aligner: bwa
    mark_duplicates: true
    realign: false
    recalibrate: false
    variantcaller:
    - freebayes
    - gatk-haplotype
    - varscan
    svcaller: 
    - lumpy
    - manta
    - cnvkit
    - metasv
    ensemble: numpass:2
  analysis: variant2
  description: T-LA-F03_S17_PE_cutadapt_QC
  files:
  - /mnt/nfsfile/yourgene-academic-workspace-pool2/zhenghank/All_projects/OD20171203-CLA252/bcbio_test/T-LA-F03_S17_PE_cutadapt_QC_R1.fastq.gz
  - /mnt/nfsfile/yourgene-academic-workspace-pool2/zhenghank/All_projects/OD20171203-CLA252/bcbio_test/T-LA-F03_S17_PE_cutadapt_QC_R2.fastq.gz
  genome_build: Lactobacillus_pentosus_SLC13
fc_name: OD20171203-merged
upload:
  dir: ../final