CLC Bio Variant detection with a Polyploid

Question

[doconnor1874]

I have a sample from a cultivated tetraploid and the reference genomes I am working with are the two diploid progenitors. I am running Basic Variant Detection on the sample against one of the diploid references and then I will run it against the other diploid.

Should the ploidy setting be 2 or 4? I thought it should be 2.

[Devon Ryan]

CLC is a commercial product, ask their paid support staff.

[apelin20]

I agree with asking their support stuff. But as a side note, whatever the ploidy is, I would suggest getting an allele frequency spectra, to get a feel of your data. This is NGS right?

Answer 1

[SES]

I agree with Devon that you should ask, but they may not be able to give you a direct answer. If it were my project, I would try both settings and compare the results. You will probably learn something about your data and their tools that way. In which case, you may be able to convince yourself which is the more reasonable setting for the data.

Answer 2

[Jonathanjacobs]

2 is the correct answer. ;)