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How do I read a haplotype string?

Rachel Colquhoun edited this page Jan 19, 2022 · 1 revision

Haplotype barcodes are strings which summarize the allele found at each of the defining sites for a constellation. They include one character per mutation/site (in order). My default:

  • - represents a ref call
  • X represents an ambiguous allele where one or more of the underlying nucleotides was an ambiguous base
  • ? represents an insertion site (these are not typed)
  • a number represents the number of deleted bases found at that site in amino acid space
  • Any other character represents either the alt allele or another (non-ref, non-alt, non-ambig) allele found at the site.