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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
The text was updated successfully, but these errors were encountered:
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
The text was updated successfully, but these errors were encountered: