bam_to_mods outputs methylation levels from ML/MM tag formatted bam files to tab separated file,
similar to modbam2bed from Oxford Nanopore. The main
dependence for bam_to_mods is fairly recent htslib (at least version 1.16).
usage: debug/bam_to_mods [-c 209] [-C 46] [-b 7] [-q 20] [-E 1796] [-m CG+m.0] [-R chr1:1-100] [--no_header] [--no_phase] [--split_strand] -r ref.fasta -i input.cram
-c|--min_mod_prob Minimum probability of modification called modified (range 0-255)
-C|--max_mod_prob Maximum probability of modification called unmodified (range 0-255)
-b|--min_baseq Minimum base quality considered.
-q|--min_mapq Minimum mapping quality considered.
-E|--exclude Exclude all reads matching any of these SAM flags.
-R|--region Genomic region to consider.
-r|--reference_fasta FAI indexed fasta file of the reference genome.
-i|--input Input SAM/BAM/CRAM file. Indexed if used with -R.
-m|--mod DNA modification to consider. Format: 'CG+m.0' for methylation 'm' of C:s on position '0'
of context 'CG' in forward strand. Can be given multiple times. If none given, 'CG+m.0' is used.
--split_strand Report modifications on either strand separately.
--no_header Don't output header text.
--no_phase Don't use HP and PS tags to separate phased reads.
-@ Extra threads for reading input.
-h|--help Print this help text.
Using htslib version 1.16.