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--- Aborted Job ---
  The genotype probability distribution in the input file does not match the reference
  panel frequencies well. The number of genotypes expected with low frequencies under HWE
  (with P<=0.1) is too big in the user data: 0.32 whereas the threshold is 0.26. For comparison,
  the number of these genotypes in 1000Genomes data is 0.17, the attached plot shows typical
  GT distributions

  This is usually an indicator of REF,ALT alleles being on incorrect strand. Another frequent
  problem is the VCF using a different reference sequence, for example GRCh38 instead of GRCh37.