how to obtain copy number info in an exome sequencing data analysis pipeline

[jie]

Hi,

I'm new to exome sequencing data analysis, and I'm puzzled by the fact that the tool packages I have (GATK, samtools) only output the CNV locations instead of the true copy numbers for each exome, or each gene. Is there any tool that can give me the copy numbers for an exome or a gene?

Besides, if I have two samples, can I directly compare their copy numbers, or I should apply some sort of normalization first?

Thank you very much for the help!

Jie

[JackieBadger]

Depends on how you are identifying copy number. I think the paper below says that using depth comparisons is not very reliable. If not there is a recent paper out there that says just that. In any case, you need a control.

http://bioinformatics.oxfordjournals.org/content/early/2012/08/29/bioinformatics.bts535.abstract

[jie]

Thank you very much!

I have read the paper. It listed all the challenges that may mess up the copy number computing. But my question is, whatever algorithm a program used (e.g. reading depth), there has to be a copy number calculate for each exome btw two samples in some point of the pipeline so that the program can call a CNV. But why that copy number never output to the final result, and is there a way to configure the pipeline (such as in Samtools or GATK) to pull that copy number out?

Jie

[arcolombo698]

Calculating the CNV

I am interested in the same problem. Have you any recommendations? I am using ANNOVAR, can GATK call the CNV?

I only know that the raw VCF file does calculate the read depth, and am not sure how the read depth relates to the CNV?