Hey everyone,
I'd like to verify if a single nucleotide variation (SNV) is in linkage disequilibrium to a 2 alleles copy number variation of 16bp (CNV). I need a program which I can input my data, and an example of an input file to run the software.
Thank you !
Lots of programs estimate linkage equilibrium. Arlequin does it, and has a great user manual:
http://cmpg.unibe.ch/software/arlequin35/Arlequin35.html
So you have 2 loci with 2 alleles, one is a SNP, and the other is an Indel? Maybe I'm thinking of this wrong but I wonder if you couldn't use a simple Fisher exact test with your SNP alleles as rows and your Indel alleles as columns?
Joel D Anderson, thank you for your answer!
Is it possible to show a preferential association of the alleles of 2 different variants with Fisher's exact test, as it is possible to do with LD calculation?
I would try Arlequin. Now that I'm thinking of it, I think you'd need to have gametic phase information in order to use a more conventional statistical approach like an exact test or Chi-square. Here is a good reference for using a Chi-square test:
https://www.ncbi.nlm.nih.gov/books/NBK22084/
The Arlequin help manual also has a good discussion of the options available if gametic phase is known or unknown.
Joel D Anderson ,If I send you some data, could you perform the LD calculation and plot?
Please!
I think this is something you could do easily yourself. Another option is the web version of Genepop. You can cut/paste your data directly and get your results back via HTML:
https://genepop.curtin.edu.au/index.html
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