Hello everyone,

So I have the genotyping results of some SNPs and INDELs done by PCR (so I only have the genotypes in Excel) and I would like to do haplotype association and LD block plot analysis on them. However, to use Haploview, it is necessary to transform them into the PED file format. It asks me to put the genotypes as 1=A, 2=T... which wouldn't work bc of the INDEL

I also look into R packages like haplo.stats but its also transform to numbers, so I'm not sure if the result would be correct.

Has anyone experienced something similar? How did you solve it?