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Plink --freq function

I have a set of files, with the names yripublished.bed, yripublished.bim, yripublished.fam

I got the frequencies of SNPs in these files with the following command:

/usr/local/sw/plink-1.90/plink --bfile yripublished --bed yripublished.bed --freq

This gives an output, where each SNP is defined by its rs ID. I need positions, not rs IDs. How can I accomplish that?

plink
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updated by chrchang523 chrchang523 • written by cetin.m cetin.m

Map file for SNPs (something like yripublished.bim) would have the positions already?

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written by zx8754 zx8754

Yes I see the positions there. But I don't know how to replace the rs IDs with them.

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written by cetin.m cetin.m

bim file and the output of --freq file match row by row, so just use paste:

paste myfile.bim myfile.freq > myResult.txt
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written by zx8754 zx8754

.bim files don’t have a header line, while the —freq output file does, so a bit more scripting would be required.

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written by chrchang523 chrchang523

1 answer

Two ways to do this:

  1. Use a short shell script to paste in positions from the .bim file. If you do this, you need to account for the fact that .bim files don’t have header lines, while the --freq output file does.

  2. Use plink 2.0 --freq cols=+pos. plink 2.0 commands have optional output columns.

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updated by zx8754 zx8754 • written by chrchang523 chrchang523

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