Software For Assessing Correlation Of Cnvs And Phenotype (I.E. Cnvwas)

Question

[pmoney1]

Hi,

I'm wondering what the best software is to do a CNVwas? I.e. a GWAS with CNV data instead of SNP data?

I have CNV data from Affy Genome-Wide Human SNP Array 6.0 that was preprocessed using the DNAcopy package in R and its in the following format

sampleName | chromosome | start | stop | numberOfProbes | log2CNV

Thanks!

Answer 1

[Matt Shirley]

Check out CNVineta. It's a straightforward R package, hasn't been updated in a while, but I did successfully use it with Affymetrix GW6 arrays in this publication. You'll need the CEL files for the arrays, though.

Also, I know PLINK has some common CNV functionality, but it looks unfinished.

Update: I also missed this one - CNVruler - it looks pretty capable.

Answer 2

[jglessnd]

Try ParseCNV