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Old 06-20-2016, 11:25 AM   #1
Location: ca

Join Date: Nov 2014
Posts: 11
Default PLINK: merge bed/bim/fam files error


I was trying to merge several files (each chr has separate file) into one big file. I gave the following command:

plink --noweb --bfile T2.chr1 --merge-list mylist.txt --make-bed --out T2

but get the following error:

ERROR: Cannot merge files. Check your MAP files.

mylist.txt contains:

T2.chr2.bed T2.chr2.bim T2.chr2.fam
T2.chr3.bed T2.chr3.bim T2.chr3.fam
T2.chr4.bed T2.chr4.bim T2.chr4.fam

All the individual .fam files appear to be identical (same file size).

What am I doing wrong?

bsmith030465 is offline   Reply With Quote
Old 06-30-2016, 03:54 AM   #2
Location: Newcastle Australia

Join Date: Mar 2013
Posts: 26

Hey mate

First suggestion I would be using plink 1.9 (don't have to worry about the annoying --noweb )

Try a process of elimination.. do a basic loop to to merge each chromosome separately until you find the troublesome file

But if it is error is related to a map file I am unsure why it is asking for that format.. you could try to --recode the data into Ped format and try merging...

Just make sure in your mylist.txt that you use a tab separator

This is a basic script out of one of my pipelines that might help you or might be totally useless but here it is anyways

for i in {1..22}


plinknew --ped chr"$i".ped --map chr"$i".map --make-bed --noweb --out chr"$i"


ls *.bed > bed.txt
ls *.bim > bim.txt
ls *.fam > fam.txt

paste bed.txt bim.txt fam.txt | column -s $'\t' -t > merge.temp.list

grep -v -w "chr1." merge.temp.list > merge.list

plinknew --bfile chr1 --merge-list merge.list --make-bed --out P67_raw

Hope that helps in some way

dickie_ho is offline   Reply With Quote

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