Standard way to represent represent indel (insertion or deletion) alleles within a haplotype
I have genotypic data that includes an indel, rs72552763, with REF allele = ATGAT and ALT allele = AT. Given Haploview v 4.2 does not support indels, have denoted the alleles as ATGAT = T and AT=C so that it is a 'pseudo-SNP'. How can I represent the T and C alleles within the haplotypes using the actual alleles?
For example, one the haplotypes is CTACTAAGGG, where T is the REF allele ATGAT.
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