(beginner) Where to find a good tutorial for QC in gwas data, genotype imputation

Question

[Laura]

Hello,

I have recently started reading and working with bioinformatics and still have little knowledge in the area (dont have programming background). I wish to evaluate some SNPs of interest in GWAS data from dbgap. I’ve downloaded some programs (plink, haploview, mach). I read and performed many software’s tutorials, but I’m having trouble in stablishing how to perform the whole analysis correctly, step by step.

Is there any tutorial for beginners? One that could guide me through basics, such as performing QC, inferring missing SNPs of interest (tagging or imputation), performing association tests.

Thank you very much!

Answer 1

[alesssia]

I found this chapter really useful: "Weale, Michael E. "Quality control for genome-wide association studies." Genetic Variation. Humana Press, 2010. 341-372." (http://link.springer.com/protocol/10.1007/978-1-60327-367-1_19 )

[Laura]

Unfortunately this chapter isn’t available in my university. But thanks for answering!