example.params.yaml

references:
  cont_vcfs:
    CHS: /genomes/GRCh38/SGVP_MAF0.01.MAS.sites.vcf.GRCh38.liftover.gz
    INS: /genomes/GRCh38/SGVP_MAF0.01.INS.sites.vcf.GRCh38.liftover.gz
    MAS: /genomes/GRCh38/SGVP_MAF0.01.CHS.sites.vcf.GRCh38.liftover.gz
  dbsnp: /genomes/GRCh38/gatk-bundle/dbsnp_146.hg38.vcf.gz
  g1k: /genomes/GRCh38/gatk-bundle/1000G_phase1.snps.high_confidence.hg38.vcf.gz
  genome: /genomes/GRCh38/gatk-bundle/Homo_sapiens_assembly38.fasta
  hapmap: /genomes/GRCh38/gatk-bundle/hapmap_3.3.hg38.vcf.gz
  mills: /genomes/GRCh38/gatk-bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
  omni: /genomes/GRCh38/gatk-bundle/1000G_omni2.5.hg38.vcf.gz
  calling_interval_list: /genomes/GRCh38/gatk-bundle/wgs_calling_regions.hg38.interval_list
samples:
  WHH2312:
    readunits:
      myreadunit:
        flowcell_id: null
        fq1: WHH2312_HS006-PE-R00076_L006_R1.fastq.gz
        fq2: WHH2312_HS006-PE-R00076_L006_R2.fastq.gz
        lane_id: '6'
        library_id: WHH2312
        rg_id: HS006-PE-R00076.6
        run_id: HS006-PE-R00076
    # more readunits
  # more samples