Output of mosdepth, covtobed and bedtools genomecov from the ../demo.bam file
covtobed ../demo.bam > covtobed.bed
bedtools genomecov -bga -ibam ../demo.bam > bedtools.bed
mosdepth mos ../demo.bam && zcat mos.per-base.bed.gz > mosdepth.bed && rm mos.*For the given example, covtobed and mosdepth produce an identical output, while bedtools will print the first line of covtobed at the end of its output.
See Wiki: implementation to understand the potential source of difference between the tools.