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From Impute2 to PLINK: when to merge chromosome files?

After Impute2, I'll have one file for each chromosome. I saw that PLINK can take each file, convert form binary, and then in another step merge them. Is this the best way to merge the chromosome files? Or is it better to merge the files before PLINK?

Thanks!!

imputation impute2 plink gwas
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updated by Wietje Wietje • written by whit18 • whit18

2 answers

I suppose it is safe to convert them in PLINK and then apply merge. I recommend the merge-list option which allows you to merge several files in one go.

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written by Wietje Wietje

Great, thanks! I can't find any good alternatives, but I'll definitely try merge-list

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written by whit18 • whit18

See GTOOLS merge -M option.

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written by zx8754 zx8754

Hi, I have used this option to merge two chromosomes as an example. I'm getting a difference in number of snps in the combined file (I suppose it should be equal to sum of the lines two files that I merge, for example. Right?)

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written by enigmargs • enigmargs

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