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Variant calling using a phased genome as reference


I want to do variant calling in a diploid organism using a phased genome as a reference. Therefore, in the reference we have both chromosomes represented. For variant calling with Haplotype Caller should I consider this genome as a diploid (as it is) or a haploid (as the reference has the 2 homolog chromosomes)? What do you think?

Thanks in advance!

Best Answer


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