offers options for setting ploidy and genetic code (see figure 26.16
Figure 26.16: Ploidy and genetic code.
- Maximum expected alleles. This is the ploidy of your organism or
better the expected maximum number of expected alleles. If set to 1, only
homozygote alleles are reported even if another allele is present as well. For
cancer samples, which often have a lot of genome duplications, we recommend a
setting of 3. For polyploid organism like plants, a setting of 4 should be used.
- Genetic code. For the table report, the variant's effect on the protein level is calculated, and the translation table specified here is used. When reporting the variant as a track, this setting has no effect, since the amino acid consequences are calculated separately (see Amino acid changes).