# Get all CpGs, then limit to the region of interest, chr11:5,241,899-5,260,650
cut -f 1-3 haptagged_cpg_track.combined.bed > cpg_profile.tsv

printf "chrom\tstart\tend\n" | cat - cpg_profile.tsv > cpg_profile_header && mv cpg_profile_header cpg_profile.tsv

# Run methbat
/mmfs1/gscratch/stergachislab/bohaczuk/analysis/hbg_lieber/ft_reruns/cpg/methbat/methbat-v0.9.0-x86_64-unknown-linux-gnu/methbat profile \
	--input-prefix haptagged_cpg_track \
	--input-regions cpg_profile.tsv \
	--output-region-profile haptagged.tsv

