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
4.
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. SNPTestReference Panel: 1000G Phase 1 v3 Shapeit2 (no singletons)
Phasing: Eagle (phased output)
Population: EUR
mode: quality control & imputation
4.
Code:
#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