# bedtools coverage - Report the depth at each position in each A feature

I am using bedtools coverage to compute the sequencing depth at every positions of a chromosome but it didn't work as I expected. Instead it reported 0 coverage at every positions.

This is how I did it :

I made a chr1.bed bedfile :

chr start   end
1   1   158534110


I ran this command :

coverageBed -a -d chr1.bed -b aln.bam -s > coverage.perposition_chr1.tsv


However I don't find any position in the output that is actually covered :

chr start end 1-pos depth
1   1   158534110   1   0
1   1   158534110   2   0
1   1   158534110   3   0
1   1   158534110   4   0
1   1   158534110   5   0
1   1   158534110   6   0
1   1   158534110   7   0
1   1   158534110   8   0
(...)
1   1   158534110   158534109   0



I must do something wrong because I already computed depth at specific pattern positions using the same aln.bam and it was working fine...

Suggestions and tries :

• Swapping -a & -d parameters produces the same results
• Adding a strand column to the bedfile still gives 0 coverage.

chr1.bed

1       1       158534110       .       0       +
1       1       158534110       .       0       -


output


1       1       158534110       .       0       +       1       0
1       1       158534110       .       0       +       2       0
(...)
1       1       158534110       .       0       -       158534108       0
1       1       158534110       .       0       -       158534109       0
$$$$

• In your .bam file (and the original reference you used) are the chromosomes called '1' '2'; etc, or 'Chr1', 'Chr2' etc? Also, you could try swapping the -a and -d - maybe the -a needs to be immediately before the .bed file. Nov 12 '19 at 17:18
• @JonathanMoore I bet you're right. The -a expects a string, so that would take -d as the value for -a. Probably worth an answer already. Nov 12 '19 at 17:21
• @JonathanMoore Yes this is the right chromosome name. I tried swipping parameters and it did produce the same file. @terdon wouldn't I expect an error If it indeed took -d as the -a value ? It is not fitting the right format Nov 12 '19 at 17:42
• Consider posting 1-2 alignments in sam format, which you would expect to give non-zero coverage as the minimum reproducible example. What is the bedtools version? What happens if you drop -s`? Nov 12 '19 at 22:52
• @TimurShtatland Dammit that was it, the bam went blank at some point in my testing. I should have suspected that. It works now. My bad and thanks all for the suggestions.. Nov 13 '19 at 9:53