# GLnexus config for joint calling DeepVariant whole exome sequencing gVCFs.
# See https://github.com/dnanexus-rnd/GLnexus/wiki/Configuration
unifier_config:
    min_AQ1: 35
    min_AQ2: 20
    min_GQ: 20
    monoallelic_sites_for_lost_alleles: true
    max_alleles_per_site: 32
genotyper_config:
    required_dp: 0
    revise_genotypes: true
    allow_partial_data: true
    more_PL: true
    trim_uncalled_alleles: true
    liftover_fields:
        - orig_names: [MIN_DP, DP]
          name: DP
          description: '##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">'
          type: int
          combi_method: min
          number: basic
          count: 1
          ignore_non_variants: true
        - orig_names: [AD]
          name: AD
          description: '##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">'
          type: int
          number: alleles
          combi_method: min
          default_type: zero
          count: 0
        - orig_names: [GQ]
          name: GQ
          description: '##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">'
          type: int
          number: basic
          combi_method: min
          count: 1
          ignore_non_variants: true
        - orig_names: [PL]
          name: PL
          description: '##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled genotype Likelihoods">'
          type: int
          number: genotype
          combi_method: missing
          count: 0
          ignore_non_variants: true