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!
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written
by
pmoney1 •
2 answers
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.
Try ParseCNV
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