Can AlphaPeel handle multiple alleles at a locus?

[gregorgorjanc]

Discussion today raised a question how to handle multiple alleles at a locus, for example STR/micro-satellite alleles.

Since AlphaPeel works with multiple biallelic SNPs, we could convert a single multi-allelic locus into a cluster of multiple biallelic SNPs leveraging binary encoding. By tweaking the map position of these loci we could ensure recombination rate is effectively zero for such a cluster.

The above would enable combining older sets of STR markers with newer sets of SNP markers.