I ran VarTrix in consensus and alt_frac modes on the same data. The output is the same size. However, I get a few NaNs in the alt_frac matrix. I am especially concerned because the number is very low (11 from a 156x3700 matrix). I assumed it was the cells with with no read coverage, but the number is too low and it does not match 0s from the consensus matrix. Is that an error or do they indicate something?
On a related note, it seems the cells with no read coverage are reported as 0. Is there a way to differentiate between true 0s and no reads?
I ran VarTrix in
consensusandalt_fracmodes on the same data. The output is the same size. However, I get a fewNaNs in thealt_fracmatrix. I am especially concerned because the number is very low (11 from a 156x3700 matrix). I assumed it was the cells with with no read coverage, but the number is too low and it does not match 0s from the consensus matrix. Is that an error or do they indicate something?On a related note, it seems the cells with no read coverage are reported as 0. Is there a way to differentiate between true 0s and no reads?