Comparing CNAs from two groups

Question

[a.beggs]

Hi

I have a sample set with two groups, e.g. case vs. controls.

I have a list of CN calls for each sample but I want to aggregate them and pull out recurrent CNAs in the dataset, ideally with statistical significance

I thought about using multiIntersectBed but obviously this won't permit statistical testing.

I can't see any obvious packages searching through the usual sources.

Any suggestions gratefully received.

[a.beggs]

Thanks! Very useful.

[Ryan D]

Just curious if your CNAs all have identical breakpoints or not. What is the minor allele frequency threshold you are using? We typically examine only those CNVs with 5% MAF or higher.

Answer 1

[Istvan Albert]

Bedtools has a new method called 'fisher' to test for statistical significance of overlaps http://bedtools.readthedocs.org/en/latest/content/history.html