Selecting Specific Snps An Imputed Genotype File

Question

[Sheila]

I have a large imputed GWAS dataset, however I would only like to continue my analysis with only some of the SNPs. I used Mach to impute my data and all files remain in this format. What programs can take a list of SNPs and retrieve these genotypes from my imputed data set?

Answer 1

[zx8754]

See How to analyze imputed GWAS data

Also, Analysis of dosage data, read in the dosage files and try --extract?

[Sheila]

Thanks for your thoughts. yes, I've seen that previous post but it wasn't helpful :( . I need to filter for specific SNPs in the imputed file (done by Mach) and run my GWAS on those. Do you know if --extract works with dosage files in Plink?

[Sheila]

I tried this and the --extract command doesn't work. Any other thoughts?

[fatima]

Could you find the solution? I have imputaed SNPs file in Minimac3 and I'd like to extract a especial set of imputed SNPs. Which software or method you used?

Thank you.