Correction for removing duplicated SNPs.

choishingwan / PRS-Tutorial

A tutorial on how to run basic polygenic risk score analysis

MIT License

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Correction for removing duplicated SNPs. #23

Closed MCorentin closed 3 years ago

MCorentin commented 3 years ago

The method to remove duplicated SNPs with grep has two issues:

"grep -v" removes the SNP entirely from the file (it would be better to just remove the duplicated lines).
grep can match unrelated SNPs (eg: if "rs13598" is duplicated, grep will also remove "rs135984", "rs135986" etc...)

Changed "grep -vf" to "awk '!seen[$3]++'" which will print each line, if the key $3 (column 3 = SNP ID) was not seen before.

MCorentin commented 3 years ago

Yes, the way you wrote it is more clear. There are a few typos ("aawk" instead of "awk") and ($1 instead of $3, to be consistent with the explanation below).

choishingwan commented 3 years ago

Thanks, that's fixed now