question about major_cn in TSV input file

[repick chen]

Hi, Andy

I was confused about the "major_cn" in TSV file.  In the usage page , it says   that major_cn is the major copy number of the cancer cells.

With cnvkit, i could calculate the copy number of some genes or some regions. But , how could i get the cn of a single mutation site.  

Maybe,  the major_cn of a certain mutation sites could be represented by gene or region including this site ?

Looking forward for your help.

cheers

Repick

[Andrew]

Hi Repick,

The copy number of a mutation is the copy number of the overlapping CNV segment. You need to look up which segment the SNV falls in to extract this value.

Cheers,

Andy