Cnv Frequency In Dgv Database

Question

[Tky]

I went through some papers which use DGV to remove common CNVs found in general population. My question is after download the DGV dataset, how to determine which CNVs has frequency > 1%. Is there any handy tools to use in this situations ?

Thank in advance.

DGV dataset for hg18:http://projects.tcag.ca/variation/tableview.asp?table=DGV_Content_Summary.txt

Answer 1

[Irsan]

Convert the CNV results of your study to .bed-format, convert the DGV-download to .BED format and use bedops suite to determine the intersection of both files (in this case, the common CNV regions). Read the documentation of the bedops suite on the website or have a look at A: Annotating Genomic Intervals

Answer 2

[Matt Shirley]

You may want to look at the downloadable tables for hg18. There is a frequency column that may be helpful.

[Tky]

Hi, Matt, thank you for the pointing this ! the frequency column is not available for all the tracks in this list, the count of the CNV is available but only the study wise sample size is given, I am wondering can I use count/(total sample number in DGV) to get the frequency.