README.md

What is DeepVCF?

A deep learning SNP variant caller aimed for Prokaryotic genomes!

Prerequisites

WARNING :: Tensorflow stable does not work with python 3.9 yet!

Install

git clone git@github.com:tmsincomb/DeepVCF.git
pip install -e ./DeepVCF

Optional Install

For creating in silico datasets

conda install -y dwgsim samtools bcftools bwa

Usage: Init

from DeepVCF.core import DeepVCF

deepvcf = DeepVCF()

Simple Usage: Variant Calling

deepvcf.train(reference_file, alignment_file, vcf_file)  # vcf treated as truth 
vcf_df = deepvcf.create_vcf(
    reference_file=query_ref_file,   
    alignment_file=query_align_file,
    output_folder='./',  
    output_prefix='my-variants'  # auto adds .deepvcf.vcf to end of file created
)
vcf_df.head() # shows pandas DataFrame for variant outputs

Tutorials

Recreating Example Datasets
Usage Demo with In Silico datasets
Model Validation with human datasets from GIAB