Question: bam-readcount tool: output zero coverage bases
0
gravatar for user230613
19 days ago by
user230613200
Europe
user230613200 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 • 92 views
ADD COMMENTlink modified 7 days ago by Chris Miller18k • written 19 days ago by user230613200
1
gravatar for Santosh Anand
19 days ago by
Santosh Anand1.5k
Santosh Anand1.5k wrote:

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

ADD COMMENTlink written 19 days ago by Santosh Anand1.5k

You're right. My mistake :/

ADD REPLYlink written 19 days ago by user230613200
0
gravatar for Chris Miller
7 days 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 7 days ago by Chris Miller18k
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