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Include noise from heterozygous / tri-allelic sites #9

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ionox0 opened this issue Jul 22, 2020 · 0 comments
Open

Include noise from heterozygous / tri-allelic sites #9

ionox0 opened this issue Jul 22, 2020 · 0 comments

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@ionox0
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ionox0 commented Jul 22, 2020

Separating this into a separate issue, as it is a bit more complicated than I originally though, and want to get it right before coding it.

Currently, the noise calculation works by designating the most common base as the "genotype" at that position, and if any of the other 3 bases pass the "threshold" (2%), that position is skipped.

We thought it might make sense that instead of skipping heterozygous / tri-allelic sites, that these rules should apply:

  • if there is an A at 49% and T and 49%, the alt allele count should still include the C at 1% and G at 1%

  • if there is an A at 33%, C at 33% and T at 33%, the alt allele count should still include the G at 1%

Also lets update the latex equations to describe these cases as well

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