bcbio

std_cancer.yaml

details:
  - analysis: variant2
    genome_build: GRCh37
    algorithm:
      # Alignment parameters
      aligner: bwa
      recalibrate: false
      realign: false
      mark_duplicates: true
      remove_lcr: false

      # ad hoc downsampling. Set to 100 for challenging samples
      maxcov_downsample: false
#      variant_regions: /g/data/gx8/extras/GRCh37_noalt.bed

      # QC and coverage assessent
      coverage: actionable/ACMG56
      mixup_check: qsignature

      # Variant calling, 2-out-of-3. All callers handle InDels
      variantcaller:
        germline: [vardict, strelka2, gatk-haplotype]
        somatic: [vardict, strelka2, mutect2] 
      ensemble:
        numpass: 2

      # Structural variation. No ensemble calling option here
      svcaller: [cnvkit, manta]
      svprioritize: cancer/az300

      # Extras
      tools_on: [gatk4, break-point-inspector, noalt_calling]
      tools_off: [gemini]
      vcfanno: [gemini]
upload:
  dir: ../final