Question: Merge Two Plink Transposed Files
0
gravatar for Zach Stednick
8.4 years ago by
Zach Stednick650
Seattle, WA
Zach Stednick650 wrote:

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.

gwas plink • 6.1k views
ADD COMMENTlink written 8.4 years ago by Zach Stednick650

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

ADD REPLYlink written 8.4 years ago by jvijai1.1k

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

ADD REPLYlink written 8.4 years ago by Zach Stednick650
2
gravatar for Pablo Marin-Garcia
8.3 years ago by
Spain
Pablo Marin-Garcia1.8k 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.

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
ADD COMMENTlink written 8.3 years ago by Pablo Marin-Garcia1.8k

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 ?

ADD REPLYlink written 8.0 years ago by P.NJ50

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.

ADD REPLYlink written 8.0 years ago by Pablo Marin-Garcia1.8k
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