Question: bam-readcount tool: output zero coverage bases
0
gravatar for user230613
3 months ago by
user230613240
Europe
user230613240 wrote:

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 • 171 views
ADD COMMENTlink modified 3 months ago by Chris Miller18k • written 3 months ago by user230613240
1
gravatar for Santosh Anand
3 months ago by
Santosh Anand2.7k
Santosh Anand2.7k wrote:

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

ADD COMMENTlink written 3 months ago by Santosh Anand2.7k

You're right. My mistake :/

ADD REPLYlink written 3 months ago by user230613240
0
gravatar for Chris Miller
3 months ago by
Chris Miller18k
Washington University in St. Louis, MO
Chris Miller18k wrote:

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)

ADD COMMENTlink written 3 months ago by Chris Miller18k
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