How To Run Penncnv On Data Obtained From The Illumina Omni 5 Platform.

Question

[jeansimon32]

Hello,

I am newbie in CNV calling software. I have some questions about PennCNV software:

1. How many samples should pennCNV be run on?
2. How to run PennCNV on illumina Omni5?
3. The last version of PennCNV is based on hg18. How to convert it to hg19?
4. How I can prepare PFB (Population frequency of B allele) file for Illumina Omni5?
5. I have already read the instruction on PennCNV website but it is not clear to me how to do that?

Highly appreciate your help

Jean

Answer 1

[Alex Reynolds]

Can you use UCSC's liftOver tool to convert results with hg18-based coordinates to hg19?