Per coordinate mapping from hg19 to hg38 (LiftOver)

[Varsha Dhankani]

Hello

For several of my projects, I have been trying to LiftOver data based on hg19 to hg38. For this, I would like to generate a look-up table that maps each hg19 coordinate to a hg38 coordinate. So, a table with 4 columns - hg19_chr | hg19_position | hg38_chr | hg38_position.

Does such a resource already exist? If not, could you suggest a way to generate it?

So far, I have tried to convert hg19.2bit to hg19.fa to hg19.bed, which is the input for LiftOver. Ideally, I would want this bed to be one coordinate per row, so I can call LiftOver for each row. 
I have the fasta file, but the process of converting fasta to BED is not clear to me yet. 

-- Thanks

Varsha Dhankani
Institute for Systems Biology
401 Terry Ave N
Seattle, WA

[Matthew Speir]

Hi Varsha,

Thank you for your question about mapping items from hg19 to hg38.

We're a little confused by your question, does the "hg19ToHg38.over.chain.gz " file provided on our download server, http://hgdownload.soe.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz, not provide what you are looking for? Or are you looking for something different? While it is not in the four column format you described, it does provide a mapping of regions from one assembly to another.

You can use this over.chain file with the command-line LiftOver utility like so:

    liftOver myRegionsInHg19.bed hg19ToHg38.over.chain.gz myRegionsInHg38.bed unMappedRegions 

Run the liftOver utility on the command line without any arguments to see a full usage message. This usage message describes options that you use to adjust the output.

I hope this is helpful. 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 Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group

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