How I do lift over a Plink bim file from Hg18 to Hg19.
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5.5 years ago
devenvyas ▴ 700

I've got some very old SNP data from Data Dryad. The BIM files uses coordinates from Hg18, but my dataset uses coordinates from Hg19.

I was wondering if anyone knows how to liftover coordinates in a Plink BIM file?

plink SNP • 9.1k views
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Had you searched, you would find plenty of resources, like here and here and here and here. Google even auto-fill your query for me.

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3.0 years ago
Shicheng Guo ★ 9.2k

Share my script with you. It can do liftover automatically (be careful about chrX and chrY):

# download database and script
wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/liftOver
wget http://hgdownload.soe.ucsc.edu/goldenPath/hg18/liftOver/hg18ToHg19.over.chain.gz
wget http://hgdownload.soe.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz
wget https://raw.githubusercontent.com/Shicheng-Guo/GscPythonUtility/master/liftOverPlink.py
wget https://raw.githubusercontent.com/Shicheng-Guo/Gscutility/master/ibdqc.pl
# rebuild plink file to avoid chromsome-miss-order problem
plink --bfile Th17Set1 --make-bed --out Th17Set1.sort
# space to tab to generate bed files for liftOver from hg18 to hg19
plink --bfile Th17Set1.sort --recode tab --out Th17Set1.tab
# apply liftOverPlink.py to update hg18 to hg19 or hg38
# Only works in BIRC10, Not HPC, Caused by Python version
mkdir liftOver
./liftOverPlink.py -m Th17Set1.tab.map -p  Th17Set1.tab.ped -o Th17Set1.hg19 -c hg18ToHg19.over.chain.gz -e ./liftOver
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When I running your scirpt at the end it shows this message: Converting MAP file to UCSC BED file... SUCC: map->bed succ Lifting BED file... sh: ./liftOver: cannot execute binary file Traceback (most recent call last): File "./liftOverPlink.py", line 172, in <module> makesure(liftBed(oldBed, newBed, unlifted, args.chainFile, liftOverPath), File "./liftOverPlink.py", line 64, in liftBed for ln in myopen(params['UNLIFTED']): File "./liftOverPlink.py", line 34, in myopen return open(fn) IOError: [Errno 2] No such file or directory: 'IMMUNO.hg19.bed.unlifted'

How can I solve ?

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I have the same problem as you. Have you solved it and how ? my code like this: python liftOverPlink.py --map chr1.map --out lifted --chain hg18ToHg19.over.chain.gz

but shows this: Converting MAP file to UCSC BED file... SUCC: map->bed succ Lifting BED file... sh: 1: liftOver: not found Traceback (most recent call last): File "liftOverPlink.py", line 172, in <module> makesure(liftBed(oldBed, newBed, unlifted, args.chainFile, liftOverPath), File "liftOverPlink.py", line 64, in liftBed for ln in myopen(params['UNLIFTED']): File "liftOverPlink.py", line 34, in myopen return open(fn) IOError: [Errno 2] No such file or directory: 'lifted.bed.unlifted'

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Hi did you solve the problem? I am having similar issues.

Thanks

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The http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/liftOver is the executable version and should be defined after -e $PATH to the location of the liftOver executable

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Are you all using python2 or python3? Make sure it is python2. The liftOverPlink.py and rmBadLifts.py scripts will not work properly unless you are using the older version.

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Just got a similar issue and it seems that the liftOverPlink script can't execute the liftOver binary file. You need to change the permission of the liftOver file.

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Hi,

What commands did you type?

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5.5 years ago
ml.endale • 0

Liftover does not natively process plink formatted files. But you can have a look to this wrapper: https://github.com/sritchie73/liftOverPlink/blob/master/README.md

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