dnanexus-rnd / GLnexus

Scalable gVCF merging and joint variant calling for population sequencing projects
Apache License 2.0
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Merge Error with Octopus GVCFs #239

Open DiDeoxy opened 3 years ago

DiDeoxy commented 3 years ago

Getting error:

[248444] [2020-10-06 19:13:24.830] [GLnexus] [error] Failed to genotype: NotImplemented: genotyper StringFormatFieldHelper::add_record_data

Config file:

unifier_config:
    min_AQ1: 0
    min_AQ2: 0
    min_GQ: 0
    monoallelic_sites_for_lost_alleles: true
genotyper_config:
    required_dp: 0
    revise_genotypes: false
    liftover_fields:
        - orig_names: [DP]
          name: DP
          description: '##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth at this position for this sample">'
          type: int
          number: basic
          combi_method: min
          count: 1
          ignore_non_variants: true
        - orig_names: [FT]
          name: FT
          description: '##FORMAT=<ID=FT,Number=1,Type=String,Description="Sample genotype filter indicating if this genotype was called">'
          type: string
          number: basic
          combi_method: semicolon
          count: 1
          ignore_non_variants: true
        - orig_names: [PS]
          name: PS
          description: '##FORMAT=<ID=PS,Number=1,Type=String,Description="Phase set">'
          type: string
          number: basic
          combi_method: missing
          count: 0
          ignore_non_variants: true
        - orig_names: [PQ]
          name: PQ
          description: '##FORMAT=<ID=PQ,Number=1,Type=Integer,Description="Phasing quality">'
          type: int
          number: basic
          combi_method: missing
          count: 1
          ignore_non_variants: true
        - orig_names: [MQ]
          name: MQ
          description: '##FORMAT=<ID=MQ,Number=1,Type=Integer,Description="RMS mapping quality">'
          type: int
          number: genotype
          combi_method: missing
          count: 1
          ignore_non_variants: true

Just looking to merge, not joint genotype.