Condition for "extra_mosaic_filters"

[Duc Tran]

Hi,
I was looking at the prediction code and noticed the condition for extra_mosaic_filters filter here:

DeepMosaic/deepmosaic/makePrediction.py

Lines 102 to 103 in a6a2f45

 extra_mosaic_filters = (depth_fractions >= 0.6) & (depth_fractions <= 1.7) & (segdups == 0) & (all_repeats == 0) &\ 
           (gnomads < 0.001) & (lower_CIs >= 0.5) & (upper_CIs < 0.5) 

Shouldn’t the condition (lower_CIs >= 0.5) & (upper_CIs < 0.5) always evaluate to false? It seems contradictory since the lower bound of the confidence interval (CI) should not be greater than the upper bound.

Thank you,
Duc

[Xiaoxu Yang]

Thank you for picking up the bug, Duc!

Should be upper_CIs >= 0.5 and lower_CIs < 0.5

This line was only used for the x-y pseudo autosomal regions (0.00087 of the genome) it won't affect the majority of the predictions. I fixed that and will release a new version.

Best,

Xiaoxu

[Duc Tran]

Thank you for the reply.

Duc