Merge Two Plink Transposed Files

Question

[Zach Stednick]

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.

[jvijai]

How about using "--recode" to make it SNP major format and then do a regular plink merge?

[Zach Stednick]

Thank you, this works ... I am not sure why I did not think of this earlier.

Answer 1

[Pablo Marin-Garcia]

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.

Having

• myfile1.tped
• myfile2.tped

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

[P.NJ]

Hi, I tried this command mentioned above to calculate the concordance rate plink --noweb --bfile file1 --bmerge file2.bed file2.bim file2.fam --merge-mode 6 --out myfile1vs2 but it shows "Concordance rate is nan" -> what does this mean ? Am i going wrong somewhere ?

[Pablo Marin-Garcia]

nan means "not a number" Are you sure that you have any SNP-ind genotype in common between datasets?. It could be that it can not calculate the 'rate' of concordance out of total in common because no genotypes in common so the rate is a division by 0. This is only speculation, I have never seen this error before.