Question: GWAS studies with RADSeq
1
gravatar for Picasa
3.4 years ago by
Picasa470
Picasa470 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 (http://catchenlab.life.illinois.edu/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.

http://pngu.mgh.harvard.edu/~purcell/plink/thresh.shtml

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 • 1.4k views
ADD COMMENTlink modified 3.4 years ago by alexisdereeper30 • written 3.4 years ago by Picasa470
0
gravatar for alexisdereeper
3.4 years ago by
alexisdereeper30 wrote:

You can use SNiPlay that allows to manage VCF file and proposes methods for filtering, PCA, MDS plot, structure... http://sniplay.southgreen.fr/cgi-bin/analysis_v3.cgi

ADD COMMENTlink written 3.4 years ago by alexisdereeper30
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1207 users visited in the last hour