What Is The Best Program To Determine Structural Variation (Cnv) For Illumina Omniexpress Data?

Question

[Biomed]

We have been using PennCNV to determine copy number variations from illumina snp chip data in our lab. We have recently started using Illumina Omniexpress chips. I know that we need to create a population B allele frequency file from our samples but I was also wondering if there was a better program for Copy Number Variation analysis using the data from this platform( Illumina OmniExpress) or is there a better option than PennCNV that we should look into?

1)PennCNV
2)?
3)?
...

Thanks

[jvijai]

BirdSuite from Broad Institute has beta support for Illumina 610, but no word on Omniexpress. Also for 3rd party, I think GoldenHelix supports Illumina. http://bit.ly/fw2Jjo

Answer 1

[Eminencegrise]

I worked with KaryoStudio and it was rather good. It is proposed by Illumina, have You tried that?

[Biomed]

Thanks for the suggestion. We use Genome Studio but I don't think it comes with KaryoStudio. Do you need to buy it, if so, do you know how much is it? Have you used any opensource alternatives and especially benchmarked them with KaryoStudio? Thanks

[Eminencegrise]

I had it in as a package with order ( I think there was no serial key needed as it is with Genome Studio), I will look for alternatives as I havent used any. The only problem was that older version (comes on a CD/DVD) of KaryoStudio had no plugin for UPD detection (corrected with update). KS was definately way better solution compared to Genotyping Console (Affymetrix).

Answer 2

[Cling]

Hi there... Do you know where to download penncnv .hmm, .pfb, .gcmodel for Illumina Human OmniExpress v.1 chip? Thanks!

[Biomed]

Hi, It is best if you ask new questions as well, "new questions" but here is your answer. You should use your own data to create your own pfb file using the script compile_pfb.pl that comes with penncnv package. You don't need to use a different hmm file, the old "hmmall" file works fine with omniexpress too.

Answer 3

[August]

You should use two separate "wide" methods to identify CNVRs. The two with the highest reviews and that are most commonly used in high impact papers are PennCNV and QuantiSNP. Afterward, consolidate the CNV calls into CNVRs. For each CNVR use a "deep" method to genotype your samples. I recommend CNVtools. You could also use CNVhap to do both simultaneously, but you would have to break the genome down into several hundred peices. Good luck!

Answer 4

[liutao1986]

Where can i download QuantSNP?? When downloaded from http://www.well.ox.ac.uk/QuantiSNP/ this website ,it was require an username and password... thanks