How many mutations does an MNP count as?

[tnguyensanger]

Should an MNP count as a single mutation? Or should it count as the total contiguous SNPs covered by the MNP?

In the omicron definition v0.6.1: https://github.com/phe-genomics/variant_definitions/blob/0.6.1/variant_yaml/pentagon-refining.yml

The definition contains 25 SNPs, 4 deletions, and 1 MNP. However, for a confirmed result, requires 27 mutations, 0 indels. If the MNP counts as a single mutation and deletions are not counted in the mutations-required count, then we can only ever call a sample as 'probable'.

calling-definition:
  confirmed:
    mutations-required: 27
    indels-required: 0
    allowed-wildtype: 0

[nickloman]

MNP counts as a single mutation. We'll check in on the counts!