how to set the number of segments?

Question

[SkyL]

Hi,

I am using CNVkit to detect CNVs on target sequencing data. However, I found that the output cns file merges all the exons for one gene. For example, in my bed file, I have multiple exons in cnr file for BRCA1:

gene

BRCA1|x23

BRCA1|x22

BRCA1|x21

...

in the cns file, it merged all the exons as BRCA1|x23, BRCA1|x22, BRCA1|x21... But I expected each exon has its own row in cns file. Is this a way to do that? Thanks!

[parvathi.sudha]

Hi,

I used batch option, and the input target genes were automatically split into multiple regions. I haven't used the --split option. I am curious to know, how you got the results with merged exons.

Thanks Parvathi.