Question: GWAS studies with RADSeq
gravatar for Picasa
2.9 years ago by
Picasa390 wrote:

Dear Biostar's community,

I'm performing GWAS using RADseq. I have 30 samples, my goal is to discriminate these samples using SNP variation.

I've succesfully applied Stacks ( with my data. And I got a vcf file at the end.

1) I've tried a PCA method using Plink and flashPCA but I didn't have so much result. I know that we have to LD prune our dataset before a PCA but I'm not sure about the others filtering method.

Any recommendations about default Missingness per individual, Missingness per marker, MAF, Hardy-Weinberg equilibrium treshold ?

2) Can you recommend other methods than PCA ?

snp gwas • 1.3k views
ADD COMMENTlink modified 2.9 years ago by alexisdereeper30 • written 2.9 years ago by Picasa390
gravatar for alexisdereeper
2.9 years ago by
alexisdereeper30 wrote:

You can use SNiPlay that allows to manage VCF file and proposes methods for filtering, PCA, MDS plot, structure...

ADD COMMENTlink written 2.9 years ago by alexisdereeper30
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