# name of the folder to write the results to
results: "results"

# callsets generated by Minigraph-Cactus pipeline (RAW VCFs)
callsets:
  MC:
    # Minigraph-Cactus VCF
    vcf: "MHC-49-MC.raw.vcf.gz"
    # Minigraph-Cactus graph GFA
    gfa: "MHC-49-MC.gfa"
    # TSV file specifying sex (1=male, 2=female) of each sample in input VCF. Format: <sample-name> <sex>. 
    sample_info: "sample-info.tsv"
    # prefix used for chromosome names in FASTA file. 
    reference_prefix: ""
    # Choose between: CHM13 | GRCh38
    reference_version: "CHM13"

vcfbub: "${HOME}/bin/vcfbub"