Looking for walkthrough guide on Rare Variant Association Analysis

Question

[houkto]

Hello there, I am looking for a good source (book, online tutorial/workshop, materials) on rare variant association analysis for complex disorders. I know there are tools exists such as C-alpha , SKAT and RVtest however they don't give walkthrough mainly how their software works.

Thanks in advance

[Khader Shameer]

What specific aspect of rare variant analyses are you looking for? Burden test?

[houkto]

burden test will do, i am looking how to get merged vcf of controls and patients (700 samples) through the process of doing the analysis. I saw some material online for a workshop going through preparation of data i get lost at some steps. if you have any tutorial or a book going through the whole process from vcf to significant results let me know.

Answer 1

[always_learning]

Any one? I think there is very few available resources on the Internet !!

Answer 2

[rbagnall]

Have a look at PLINK/SEQ tutorials. They give a walk through of the steps involved in exploring variation in vcf files, including different types of association tests.

You should probably start at the PLINK/SEQ_101 and the extended tutorial, which have lots of informative steps on setting up the vcf as a database, querying vcf attributes, and samples (near top of right hand column).