# Example configuration to perform variant calling with multiple methods on a set of
# NA12878 replicates. The final calls are merged into a finalized ensemble callset
# using a support vector machine based on several classifier metrics.
---
fc_date: '121119'
fc_name: cliacmp
details:
  - files: [/usr/local/projects/CLIA-Validation/secondary/NA12878-NGv3-LAB1360-A/alignment/NA12878-NGv3-LAB1360-A.bam]
    lane: NA12878-NGv3-LAB1360-A
    description: NA12878-NGv3-LAB1360-A
    analysis: variant
    genome_build: GRCh37
    algorithm:
      aligner: false
      recalibrate: false
      realign: false
      variantcaller: [gatk, freebayes, samtools, gatk-haplotype, varscan]
      ensemble:
        format-filters: [DP < 4]
        classifiers: 
          balance: [AD, FS, Entropy]
          calling: [ReadPosEndDist, PL, PLratio, Entropy, NBQ]
        classifier-params:
          type: svm
        trusted-pct: 0.65
      quality_format: Standard
      coverage_interval: regional
      variant_regions: /usr/local/projects/CLIA-Validation/secondary/NA12878-NGv3-LAB1360-A/enrichment/padded_targets_200.bed
  - files: [/usr/local/projects/CLIA-Validation/secondary/NA12878-NGv3-LAB1363-A/alignment/NA12878-NGv3-LAB1363-A.bam]
    lane: NA12878-NGv3-LAB1363-A
    description: NA12878-NGv3-LAB1363-A
    analysis: variant
    genome_build: GRCh37
    algorithm:
      aligner: false
      recalibrate: false
      realign: false
      variantcaller: [gatk, freebayes, samtools, gatk-haplotype, varscan]
      ensemble:
        format-filters: [DP < 4]
        classifiers: 
          balance: [AD, FS, Entropy]
          calling: [ReadPosEndDist, PL, PLratio, Entropy, NBQ]
        classifier-params:
          type: svm
        trusted-pct: 0.65
      quality_format: Standard
      coverage_interval: regional
      variant_regions: /usr/local/projects/CLIA-Validation/secondary/NA12878-NGv3-LAB1363-A/enrichment/padded_targets_200.bed
  - files: [/usr/local/projects/CLIA-Validation/secondary/NA12878-AGXT2-LAB1368-A/alignment/NA12878-AGXT2-LAB1368-A.bam]
    lane: NA12878-AGXT2-LAB1368-A
    description: NA12878-AGXT2-LAB1368-A
    analysis: variant
    genome_build: GRCh37
    algorithm:
      aligner: false
      recalibrate: false
      realign: false
      variantcaller: [gatk, freebayes, samtools, gatk-haplotype, varscan]
      ensemble:
        format-filters: [DP < 4]
        classifiers: 
          balance: [AD, FS, Entropy]
          calling: [ReadPosEndDist, PL, PLratio, Entropy, NBQ]
        classifier-params:
          type: svm
        trusted-pct: 0.65
      quality_format: Standard
      coverage_interval: regional
      variant_regions: /usr/local/projects/CLIA-Validation/secondary/NA12878-AGXT2-LAB1368-A/enrichment/padded_targets_200.bed
