Looking for walkthrough guide on Rare Variant Association Analysis
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4.7 years ago
houkto ▴ 80

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

next-gen SNP • 2.1k views
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What specific aspect of rare variant analyses are you looking for? Burden test?

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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.

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3.3 years ago
always_learning ★ 1.1k

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

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3.3 years ago
rbagnall ★ 1.7k

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).

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