details:
- algorithm:
    aligner: bwa
    effects: vep
    effects_transcripts: all
    ensemble:
      numpass: 2
      use_filtered: false
    mark_duplicates: true
    realign: false
    recalibrate: false
    save_diskspace: true
    tools_on:
    - gemini
    - svplots
    - qualimap
    - vep_splicesite_annotations
    - noalt_calling
    variantcaller:
    - gatk-haplotype
    - samtools
    - platypus
    - freebayes
    vcfanno:
    - /home/atheyt@med.umanitoba.ca/cre/cre.vcfanno.conf
  analysis: variant2
  description: 151002_7001448_0359_AC7F6GANXX_Sample_HG002-EEogPU_v02-KIT-Av5_AGATGTAC_L008.posiSrt.markDup
  files:
  - /home/atheyt@med.umanitoba.ca/Pipeline_Tests/Test14/AshkenaziFam/input/151002_7001448_0359_AC7F6GANXX_Sample_HG002-EEogPU_v02-KIT-Av5_AGATGTAC_L008.posiSrt.markDup.bam
  genome_build: GRCh37
  metadata:
    batch: AshkenaziFam
- algorithm:
    aligner: bwa
    effects: vep
    effects_transcripts: all
    ensemble:
      numpass: 2
      use_filtered: false
    mark_duplicates: true
    realign: false
    recalibrate: false
    save_diskspace: true
    tools_on:
    - gemini
    - svplots
    - qualimap
    - vep_splicesite_annotations
    - noalt_calling
    variantcaller:
    - gatk-haplotype
    - samtools
    - platypus
    - freebayes
    vcfanno:
    - /home/atheyt@med.umanitoba.ca/cre/cre.vcfanno.conf
  analysis: variant2
  description: 151002_7001448_0359_AC7F6GANXX_Sample_HG003-EEogPU_v02-KIT-Av5_TCTTCACA_L008.posiSrt.markDup
  files:
  - /home/atheyt@med.umanitoba.ca/Pipeline_Tests/Test14/AshkenaziFam/input/151002_7001448_0359_AC7F6GANXX_Sample_HG003-EEogPU_v02-KIT-Av5_TCTTCACA_L008.posiSrt.markDup.bam
  genome_build: GRCh37
  metadata:
    batch: AshkenaziFam
- algorithm:
    aligner: bwa
    effects: vep
    effects_transcripts: all
    ensemble:
      numpass: 2
      use_filtered: false
    mark_duplicates: true
    realign: false
    recalibrate: false
    save_diskspace: true
    tools_on:
    - gemini
    - svplots
    - qualimap
    - vep_splicesite_annotations
    - noalt_calling
    variantcaller:
    - gatk-haplotype
    - samtools
    - platypus
    - freebayes
    vcfanno:
    - /home/atheyt@med.umanitoba.ca/cre/cre.vcfanno.conf
  analysis: variant2
  description: 151002_7001448_0359_AC7F6GANXX_Sample_HG004-EEogPU_v02-KIT-Av5_CCGAAGTA_L008.posiSrt.markDup
  files:
  - /home/atheyt@med.umanitoba.ca/Pipeline_Tests/Test14/AshkenaziFam/input/151002_7001448_0359_AC7F6GANXX_Sample_HG004-EEogPU_v02-KIT-Av5_CCGAAGTA_L008.posiSrt.markDup.bam
  genome_build: GRCh37
  metadata:
    batch: AshkenaziFam
fc_name: AshkenaziFam
resources:
  default:
    cores: 7
    jvm_opts:
    - -Xms750m
    - -Xmx7000m
    memory: 7G
upload:
  dir: ../final