# To compare CpG between two samples, first label each sample with haplotype using add_bam_hap_tag.py

# Merge tagged bam files

# Run pb-cpg-tools with run_cpg_track.txt

# Make methbat profile with run_methbat.txt

# Identify polymorphisms find_polymorphisms_CG.py

# Filter polymorphisms from methbat output run_filter_polymorphisms.txt

# Make UCSC tracks for color coding with run_split_pvals.txt

