I want to look at concordance by SNP using Plink, however my two datasets are both in Plink TPED/TFAM format. the documentation on Plink merge covers regular ped and map files. Is there a way to merge these datsets as is or do I need to convert to ped/map before merging.
Question: Merge Two Plink Transposed Files
8.4 years ago by
Zach Stednick • 650
Zach Stednick • 650 wrote:
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8.3 years ago by
Pablo Marin-Garcia • 1.8k
Pablo Marin-Garcia • 1.8k wrote:
You can not use the tped in the merge. In order to save time and disk space I would recommend you to convert to bed and then do the merge-comparison.
I would do the comparison as follow:
plink --noweb --tfile myfile1 --make-bed --out myfile1 plink --noweb --tfile myfile2 --make-bed --out myfile2 # then the comparison plink --noweb --bfile myfile1 --bmerge myfile2.bed myfile2.bim byfile2.fam --merge-mode 6 --out myfile1vs2
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