Question: Looking for walkthrough guide on Rare Variant Association Analysis
6
gravatar for houkto
2.4 years ago by
houkto60
UK
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 • 1.0k views
ADD COMMENTlink modified 12 months ago by rbagnall1.4k • written 2.4 years ago by houkto60
1

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

ADD REPLYlink written 2.4 years ago by Khader Shameer18k

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 2.4 years ago by houkto60
0
gravatar for always_learning
12 months ago by
Doha, Qatar
always_learning980 wrote:

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

ADD COMMENTlink written 12 months ago by always_learning980
0
gravatar for rbagnall
12 months ago by
rbagnall1.4k
Australia
rbagnall1.4k 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 12 months ago by rbagnall1.4k
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