Question: Looking for walkthrough guide on Rare Variant Association Analysis
gravatar for houkto
23 months ago by
houkto60 wrote:

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

snp next-gen • 843 views
ADD COMMENTlink modified 6 months ago by rbagnall1.3k • written 23 months ago by houkto60

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

ADD REPLYlink written 23 months ago by Khader Shameer17k

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.

ADD REPLYlink written 23 months ago by houkto60
gravatar for always_learning
6 months ago by
Doha, Qatar
always_learning950 wrote:

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

ADD COMMENTlink written 6 months ago by always_learning950
gravatar for rbagnall
6 months ago by
rbagnall1.3k wrote:

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).

ADD COMMENTlink written 6 months ago by rbagnall1.3k
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