Removing SNPs from .bed file?

Question

[dam4l]

I have a list of imputed SNPs in a binary file (.bed, .bim, .fam) and I would like to perform some QC before proceeding with further analysis. I need to remove a list of SNPs based on low MAF and poor imputation quality (I have this list). Is it possible to remove this list from the .bed file to create a new binary fileset that no longer contains these variants?

Answer 1

[Joey]

Use PLINK (either 1.07 or 1.90).

Look at removing subset of SNPs in this page: http://pngu.mgh.harvard.edu/~purcell/plink/dataman.shtml#exclude

If you have a text file (say snplist.txt) with SNP rsIDs (no headers) containing the list of SNPs that need to be excluded from the SNP data set (example.bed, example.bim, example.fam) use the following command (in PLINK 1.07)

plink --noweb --bfile example --exclude snplist.txt --make-bed --out newdata

This will make the new file in binary format .