Question: cnvkit segmetrics on multiple files
gravatar for adoak
11 days ago by
adoak10 wrote:

Is there a way to run segmetrics on multiple files at once? or incorporate it into batch? Additionally, I have certain segments or chromosomes that keep showing up as having no variation. Is this a problem with mapping?

cnv cnvkit • 168 views
ADD COMMENTlink modified 10 days ago by Eric T.1.9k • written 11 days ago by adoak10
gravatar for Eric T.
10 days ago by
Eric T.1.9k
San Francisco, CA
Eric T.1.9k wrote:

It's not currently part of batch, so I'd recommend running it in a loop in Bash or a Makefile.

No variation, or no reads? The latter would be an issue with mapping, the former maybe not. Which chromosomes or regions are causing trouble? I'd expect that regions close to centromeres and telomeres, as well as chr6 and chrY, would be noisy. Using more samples in your pooled reference can help to both reduce noise at these regions and improve the sensitivity of calling in the rest of the genome.

ADD COMMENTlink written 10 days ago by Eric T.1.9k
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