GWAS state-of-the-art how-to?

[LeonDK]

Dear all,

Newbie here - So I have embarked on a new journey to the land of GWAS! This means that I now have a plethora of file formats and software tools, that I'll need to absorb. I am hoping for some input from the more experienced SEQanswer users

For a set of samples, we have used Illumina's Infinium OmniExpressExome-8 BeadChip Kit [1] for snp genotyping. We have then used the Michigan Imputation Server [2] to impute full genotypes. Based on the full genotypes, we wish to run a GWAS against a binary variable using SNPTEST (v2.5.2) [3]

Steps
A) Filter the imputed vcf file [4]
B) Create Genotype file for SNPTest
C) Create Sample file for SNPTest, adjusting for sex
D) Run SNPTest using -pheno -frequentist -method score

Questions
i. Reg. A) what should I filter on using which tool? MAF >= 0.05 and R2 >= ?
ii. Reg. B) I could write a script, but tools for doing this must exist?
iii. Can you recommend a good GWAS-tutorial?

...and naturally any input/comments you may have are very welcome - Thank you!

Links
1. Infinium OmniExpressExome-8 BeadChip Kit
2. Michigan Imputation Server

Software: Minimac3
Reference Panel: 1000G Phase 1 v3 Shapeit2 (no singletons)
Phasing: Eagle (phased output)
Population: EUR
mode: quality control & imputation

3. SNPTest
4.

#CHROM  POS       ID           REF       ALT  QUAL  FILTER  INFO                    FORMAT    ID
21      9411243   21:9411243   A         C    .     PASS    MAF=0.00412;R2=0.00000  GT:DS:GP  0|0:0.008:0.992,0.008,0.000
21      9825566   21:9825566   CCCGCCCG  C    .     PASS    MAF=0.04991;R2=0.00000  GT:DS:GP  0|0:0.100:0.903,0.095,0.002
21      14702903  21:14702903  ATATATAT  A    .     PASS    MAF=0.46526;R2=0.73793  GT:DS:GP  1|0:0.894:0.108,0.890,0.002