fc_date: 20HHFLHB
fc_name: HHFLHBCXX
upload:
  dir: /mnt/speed/qc/sequencing/ihg-pipeline/160208_SN404_0473_AHHFLHBCXX/Project_Exome-Validation-EV-5/ 
details:
  - files: [/mnt/speed/qc/sequencing/ihg-pipeline/Sample_R14-18102/Sample_R14-18102_R1.fastq, /mnt/speed/qc/sequencing/ihg-pipeline/Sample_R14-18102/Sample_R14-18102_R2.fastq]
    description: R14-18102_kapa-NGv3-PE100-NGv3 
    analysis: 'variant2'
    genome_build: GRCh37
    lane: R14-18102
    algorithm:
      aligner: bwa
      trim_reads: false
      recalibrate: gatk
      realign: gatk
      variantcaller: [gatk,gatk-haplotype,platypus]
      jointcaller: [gatk-haplotype-joint, platypus-joint]
      coverage_interval: regional
      coverage_depth: high
      variant_regions: /mnt/speed/qc/sequencing/biodata/capture_regions/xgen-exome-research-panel-targets-cols1-2-noChr.bed
      clinical_reporting: true
    metadata:
      batch: Batch1
  - files: [/mnt/speed/qc/sequencing/ihg-pipeline/Sample_R14-18105/Sample_R14-18105_R1.fastq, /mnt/speed/qc/sequencing/ihg-pipeline/Sample_R14-18105/Sample_R14-18105_R2.fastq]
    description: R14-18105_kapa-NGv3-PE100-NGv3
    analysis: 'variant2'
    genome_build: GRCh37
    lane: R14-18105
    algorithm:
      aligner: bwa
      trim_reads: false
      recalibrate: gatk
      realign: gatk
      variantcaller: [gatk,gatk-haplotype,platypus]
      jointcaller: [gatk-haplotype-joint, platypus-joint]
      coverage_interval: regional
      coverage_depth: high
      variant_regions: /mnt/speed/qc/sequencing/biodata/capture_regions/xgen-exome-research-panel-targets-cols1-2-noChr.bed
      clinical_reporting: true
    metadata:
      batch: Batch1
  - files: [/mnt/speed/qc/sequencing/ihg-pipeline/Sample_R14-18106/Sample_R14-18106_R1.fastq, /mnt/speed/qc/sequencing/ihg-pipeline/Sample_R14-18106/Sample_R14-18106_R2.fastq]
    description: R14-18106_kapa-NGv3-PE100-NGv3
    analysis: 'variant2'
    genome_build: GRCh37
    lane: R14-18106
    algorithm:
      aligner: bwa
      trim_reads: false
      recalibrate: gatk
      realign: gatk
      variantcaller: [gatk,gatk-haplotype,platypus]
      jointcaller: [gatk-haplotype-joint, platypus-joint]
      coverage_interval: regional
      coverage_depth: high
      variant_regions: /mnt/speed/qc/sequencing/biodata/capture_regions/xgen-exome-research-panel-targets-cols1-2-noChr.bed
      clinical_reporting: true
    metadata:
      batch: Batch1