Data format error: expecting at least 3 fields in BED file

[Peiyuan Zhu]

liftOver doesn't recognize .bed PLINK file. What shall I do? 

MacBookPro:data garyzhubc$ ./liftOver VASST.bed hg18ToHg19.over.chain.gz VASST_liftover.bed VASST_liftover_unmapped.bed

Reading liftover chains

Mapping coordinates

Data format error: expecting at least 3 fields in BED file (VASST.bed)

[Clay Fischer]

Hello Peiyuan Zhu,

Thank you for your question regarding the use of liftOver with a PLINK BED file.

A PLINK BED file is not the same thing as a UCSC BED (Browser Extensible Data) file. You can review the UCSC BED file format (http://genome.ucsc.edu/FAQ/FAQformat.html#format1) and compare this to your PLINK BED format.

If your BED file is in the correct UCSC BED format and you are still having problems, please respond to the group for further assistance. In doing so, it would be helpful for us to see a few lines from your file so that we can help verify the format.

Thank you again for your inquiry and for using the UCSC Genome Browser. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Thanks,
Clay Fischer
UCSC Genomics Institute

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