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How do I read a haplotype string?
Rachel Colquhoun edited this page Jan 19, 2022
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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:
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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.