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Selecting Specific Snps An Imputed Genotype File

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?

imputation genotype gwas
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updated by zx8754 zx8754 • written by Sheila Sheila

1 answer

See How to analyze imputed GWAS data

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

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written by zx8754 zx8754

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?

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written by Sheila Sheila

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

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written by Sheila Sheila

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.

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written by fatima • fatima

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