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rvalieris / LCS

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proportions don't sum to 1? #11

Open will-rowe22 opened 2 years ago

will-rowe22 commented 2 years ago

I've been through a couple of runs and the sums of the proportions of variants per sample don't sum to 1, is this correct?

rvalieris commented 2 years ago

hello,

depends, if you are talking about the proportions of a sample summing to less than 1 then that means there is a proportion of the "reference variant" present in the sample, all mutations are called against the sars-cov-2 reference genome which was created based on one of the very first variants observed(lineage A), so by definition this variant does not have any mutations (because its identical to the ref genome), so if the sum of proportions is, for example 0.7, that means the other 0.3 are estimated to be this "reference variant".

if you are talking about summing to more than 1, then it could be due to the numerical precision of the solver, but it shouldn't be significant more than 1.