Question: generate consensus sequence from unphased heterozygous calls
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gravatar for atul_shah1
3.0 years ago by
atul_shah10
atul_shah10 wrote:

I'd like to generate a single consensus by substituting a set of unphased snp and indel variant calls, each with specified zygosity, into a reference sequence. A heterozygous snp can be represented by an IUPAC ambiguity code from {R,Y,S,W,K,M}. Is there a standard designation of a het indel? e.g. an ambiguity code to indicate either a base or a "gap", i.e. (A,-), (C,-), etc. at a particular position? Some other community standard for designating heterozygosity? Thanks for your help!

ADD COMMENTlink modified 2.9 years ago by Biostar ♦♦ 20 • written 3.0 years ago by atul_shah10
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