how to check copy number from certain gene

[cliff]

Hi, All

I have a cell mix sample: 30 cells A + 80 cells B. I used Illuima GA to sequence this sample, and then used BWA to do mapping and SAMtools to call SNPs. Now, I want to find how many copies a certain gene has in these two cell lines (i.e., A and B).

Anyone knows a good way to find out the copy number?

I'll appreciate all your help.

-Cliff

[arcolombo698]

I am working on this same issue, did you have any progress here?

[GenoMax]

This tool was just presented at ISMB. http://www.ncbi.nlm.nih.gov/pubmed/25016581 Software is available at: https://oncocnv.curie.fr/