How to get copy number of gene from WGS data?

Question

[marksingh1982]

I am looking specifically to find the number of copies of a single gene from WGS data.

[German.M.Demidov]

if you look for simple deletions and tandem duplications, you can run Manta on your genome.

if you consider your gene complex and polymorphic, you need several other samples to establish the baseline. more complex the gene is - more samples you need as a background, up to 500. I have not seen anything that requires more than 500 samples, but there is no limit for genome complexity.