bedtools coverageBed vs samtools mpileup, speed

[akvarel]

I would like to use bedtools as it seems to have much more options for the input/output file. However, it seems that bedtools is way slower than the samtools.


I have: multiple bad files (sorted and indexed) and multiple regions and I want a coverage per base.
gene_coord_red.bed has only one region.
I ran bedtools coverageBed(v2.25.0) following:

time coverageBed -a gene_coord_red.bed -b reads.sort.bam -d > bedtools.txt
real    2m17.861s
user    1m57.572s
sys    0m19.926s

I ran samtools mpileup:

time samtools mpileup -Q 0 -l gene_coord_red.bed reads.sort.bam > mpileup.txt

real    0m23.595s
user    0m22.808s
sys    0m0.301s

Why is the bedtools running so slow? Can I accelerate it somehow?

[dpryan]

See also on biostars.