liftOverPlink output 0 bytes

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6.0 years ago

honghong0220 ▴ 10

Hi, I have the plink bfiles for SNP genotyping map to build38 and I want to convert to build 37. Here is my command

$ python liftOverPlink.py --map SHARE_MESA_AA_chr9_position.map --out lifted --chain hg38ToHg19.over.chain.gz

Converting MAP file to UCSC BED file...
SUCC:  map->bed succ
Lifting BED file...
Reading liftover chains
q end mismatch 12611573 vs 249240621 line 87 of hg38ToHg19.over.chain.gz

SUCC:  liftBed succ
Converting lifted BED file back to MAP...
SUCC:  bed->map succ
cleaning up BED files.

..

However, the output lifted.map is 0 bytes. I don't know where is wrong. Anyone has some suggestion for my problem? I am very appreciated your help!

SNP • 1.5k views

ADD COMMENT • link updated 6.0 years ago by GenoMax 141k • written 6.0 years ago by honghong0220 ▴ 10

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Try to confirm that your co-ordinates are indeed 'mappable' from hg38 to hg19 via the UCSC liftover tool: https://genome.ucsc.edu/cgi-bin/hgLiftOver

Many regions in hg38 did not exist in hg19.

ADD REPLY • link 6.0 years ago by Kevin Blighe 87k

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Thanks Kevin for your suggestion. Already solve this. The downloaded chain file has problem.

ADD REPLY • link 6.0 years ago by honghong0220 ▴ 10

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