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NeuSomatic: Deep convolutional neural networks for accurate somatic mutation detection
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adapt for ultra-deep sequencing data #78

Open WeiweiBian opened 3 years ago

WeiweiBian commented 3 years ago

Hi,

I try to adapt your model for my deep-targeted sequencing data(> 100,000X depth) for somatic mutation calling. I noticed that the default read depth is identified as 100 in the proprocess.py. https://github.com/bioinform/neusomatic/blob/master/neusomatic/python/preprocess.py#L243

I wonder whether this depth could be modified to a larger number for our deep sequencing data and whether our data can be encoded into layers for the architecture of the CNN model you built.

Thanks a lot!

Best, Weiwei