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I am reading the Online methods of the demuxlet paper.
The genotype $g$ is taken from the set $\{0, 1, 2\}$, defined as "the true genotype of the sample corresponding to $c$-th droplet at $v$-th variant". What is the mapping between these values and the corresponding genotype?
Each variant is modeled using a binomial with $n=2,p=\frac{g}{2}$, so I would assume that 1 is heterozygous, 0 is homozygous REF and 2 homozygous ALT. Is this assumption correct?
The genotypes $\{0,1,2\}$ are mappings to the genotypes AA (homref), AB (heterozygous), BB (homalt) (from supplementary resources). This is also mapped to the number of alterations (e.g., 0 -> 0 alterations -> homref).
