Merge multiple bedMethyl files

If you generate bedMethyl tables from multiple samples and want to perform a "join" where the counts summed modkit bedmethyl merge will perform an outer join for you. An example command is below:

modkit bedmethyl merge sample_a.bed.gz sample_b.bed.gz \
  -o samples_a_and_b.bed \
  -g genome_sizes.tsv # could be reference.fa.fai

The input bedMethyl files must be bgzipped and tabix indexed.

bgzip sample_a.bed
tabix sample_a.bed.gz

bgzip sample_b.bed
tabix sample_b.bed.gz

The genome_sizes.tsv is a tab-separated file containing the lengths of the contigs in the reference sequence, you can also use a .fai file generated by samtools faidx.

For example taken from bedtools:

The schema should be <chromName><TAB><chromSize>.

For example, Human (hg19):

chr1    249250621
chr2    243199373