Checking steps to analyze snp-array data for variants detection

Question

[Sharon]

Hi everyone

I would like to double check my naive steps to analyze SNP-Array data to detect variants associated with a specific phenotypes with you. It is my first go with this data.

1. I converted illumina report to plink format using genome studio.
2. Then I converted plink format to vcf.
3. I annotated the vcf from plink using annovar.
4. Then I started analyzing the data the same way I do for exome data.

It seems very naiive, so is this the best way to analyze snp-array data for aim of finding variants/genes associated with a specific type? Any tutotrials exist I am oblivious of?

Thanks

Answer 1

[Sharon]

Just in case some one is new to SNP array like me, I found this tutorial, and it is interesting and very helpful:

https://onlinelibrary.wiley.com/doi/full/10.1002/sim.6605