bam-readcount tool: output zero coverage bases

Question

[user230613]

I think the question title is self explanatory. Is it possible to output bases with zero coverage using bam-readcount tool. Something similar to samtools depth:

Usage: samtools depth [options] in1.bam [in2.bam [...]]
Options:
   -a   output all positions (including zero depth)

Answer 1

[Santosh Anand]

is it not? The README says otherwise: "This program reports readcounts for each base at each position requested."!

[user230613]

You're right. My mistake :/

Answer 2

[Chris Miller]

You are correct that bam-readcount does not output zero-coverage bases. It requires a little post-processing to add those back in. (such as what's done here https://github.com/genome/genome/blob/master/lib/perl/Genome/Model/Tools/Analysis/Coverage/BamReadcount.pm)