model=/mmfs1/gscratch/stergachislab/bin/pb-CpG-tools-v2.3.1-x86_64-unknown-linux-gnu/models/pileup_calling_model.v1.tflite

bampath=/mmfs1/gscratch/stergachislab/bohaczuk/analysis/targeted_methods_paper/DM1_cpg/DM1_normvsRE_happd.bam

/mmfs1/gscratch/stergachislab/bin/pb-CpG-tools-v2.3.1-x86_64-unknown-linux-gnu/bin/aligned_bam_to_cpg_scores \
        --threads 8 --model $model --output-prefix haptagged_cpg_track --bam $bampath
