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bam-readcount tool: output zero coverage bases

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)
bam-readcount
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updated by Chris Miller Chris Miller • written by user230613 user230613

2 answers

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

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written by Santosh Anand Santosh Anand

You're right. My mistake :/

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written by user230613 user230613

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)

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written by Chris Miller Chris Miller

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