I'm trying to do an LD analysis between SNPs and CNVs. Is there any tool that does this? I've tried PLINK and VCFtools, but neither have this option. Any help would be greatly appreciated.
Hi Benika,
Your intuition that this may be different than SNP to SNP LD is correct. In fact, it is already known that using traditional SNP-SNP LD metrics can lead to incorrect results. Thus, specific methodologies to study this have already been published for dealing with this issue, although there is not a lot out there, yet ...
You might try this resource: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3109359/ - it is a framework for determining SNP CNV LD that uses a custom method, and if it is unable to determine it with the new method it will, otherwise the program resorts to default SNV - SNV LD determination metrics.
Furthermore, in the Web Resources section, it says that the code is available on request. I believe that last author, Dr. Hemant Tiwari, is at UAB and is an active researcher, so you would likely be able to get it from him or the first author.
This paper describes the two in relation to haplotype, which would also be very good background for you: http://bioinformatics.oxfordjournals.org/content/26/11/1437.full
Beyond this, I think combing through Google and Pubmed Results will get you up to speed on what has and has not been done in this area. Good luck and let us know what you find.
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Thank you so much Vincent! I will definitely try this and read this paper. I've been stuck on this for months. Thank you!
Definitely.
Also, since their software is only available on request, if I were you I would go ahead and request it soon and anticipate a small wait... let me know what you find out.
Yes, I already did. just waiting. I will post here once I hear back.
Thanks again Vincent.
Hi Benika,
I am trying to do exactly the same as you and I am struggling finding a tool to do that. I have also sent the authors of the paper above an email and I am waiting for a response, but since you have faced this problem 3 months ago, can you please tell me if you found a solution to this?
Any help will be greatly appreciated.
Thank you!!