Question

From Impute2 to PLINK: when to merge chromosome files?

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7.0 years ago

whit18 ▴ 20

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 • 3.5k views

ADD COMMENT • link updated 7.0 years ago by Wietje ▴ 240 • written 7.0 years ago by whit18 ▴ 20

score 1 · Answer 1 · 2018-01-08

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7.0 years ago

Wietje ▴ 240

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.

ADD COMMENT • link 7.0 years ago by Wietje ▴ 240

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

ADD REPLY • link 7.0 years ago by whit18 ▴ 20

score 1 · Answer 2 · 2018-02-25

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6.8 years ago

zx8754 12k

See GTOOLS merge -M option.

ADD COMMENT • link 6.8 years ago by zx8754 12k

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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?)

ADD REPLY • link 4.7 years ago by enigmargs • 0