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Overall non-diploid ratio (OND)
The formula and the description given for the OND annotation seem to be contradictory (see: https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_annotator_AlleleBalance.php). The formula implies that a true diploid variant would have a non-allele value of zero and therefore have an OND=1. However, the description "reads that support something other than the genotyped alleles (called "non-alleles") will be counted in the OND tag, which represents the overall fraction of data that diverges from the diploid hypothesis." suggests that a higher fraction is more divergent from diploid. Can you please clarify (e.g., confirm the true formula should be 1-alleles/(alleles+non-alleles) and that an ideal diploid variant would have an OND of zero)?
Additionally, we have noticed a lot of missing OND values (not multiallelic or indels). Can you explain when/why these may be missing?
Thanks so much!