Hi,
I'm analyzing chloroplast SNPs and about 66% (44 our of 66) were
heterozygous SNPs. As the chloroplast's genome is haploid it would be
considered heteroplasmy. My question is that for haplotype analysis,
clustering or principal components should I take out the SNPs that show
heteroplasmy or should I use all the set?
Thanks for your advice in advance.
With regards,
Jorge
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