Question

Selecting Specific Snps An Imputed Genotype File

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11.5 years ago

Sheila ▴ 460

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 • 3.8k views

ADD COMMENT • link updated 11.5 years ago by zx8754 12k • written 11.5 years ago by Sheila ▴ 460

score 1 · Answer 1 · 2013-05-21

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11.5 years ago

zx8754 12k

See How to analyze imputed GWAS data

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

ADD COMMENT • link 11.5 years ago by zx8754 12k

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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?

ADD REPLY • link 11.5 years ago by Sheila ▴ 460

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

ADD REPLY • link 11.5 years ago by Sheila ▴ 460

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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.

ADD REPLY • link 8.1 years ago by fatima ▴ 20