STRonvoli

CNN for enhancing short read STR calls

Pre-processing steps:

• One-hot encode bases at each position
• Custom Dataset, Dataloader for base, depth, metadata

3 methods:

1. Baseline CNN -> FCN with concatenated metadata
2. Dilated self-designed kernel in CNN -> FCN w/concatenated metadata
3. 2 convolutional networks with regular kernel -> aggregate -> FCN w/concatenate metadata

We are maintaining same number of convolutional/FCN layers and number of kernels for the 3 models so they aren't confounding.