hg18 to h19 leftover failure

[Lakshman Kumar, Preeti]

Hi Team,

I’m trying to convert hapmap3 (.bed) from hg18 to h19 using liftover, I tried both the online version as well as the command line version but fails to do the conversion. Please help me with this at the earliest.

 

 

Thanks,

Preeti Lakshman Kumar

Bioinformatician I,

Division of Pulmonary, allergy and critical Care

701 19th Street S, LHRB 440

Birmingham, AL 35233

T: 205-934-0715

[Jairo Navarro Gonzalez]

Hello Preeti,

Thank you for using the UCSC Genome Browser and your inquiry.

The LiftOver tool can convert coordinates between assemblies using either our BED or chrN:start-end formats. If you are unfamiliar with our BED format, you can learn more about it from the following help page. You may also be interested in the following HapMap SNPs track on hg19 with the data coordinates lifted from hg18:

http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=hapmapSnps

The failed conversion could be due to a confusion on the BED format that the LiftOver utility accepts. For example, you may be using a different version of BED (PLINK format) which is not compatible with the LiftOver utility. Here is a previously answered question that you may find useful:

https://groups.google.com/a/soe.ucsc.edu/d/msg/genome/AgxiAeeKSd8/eVejPZXlDgAJ

If after reviewing these help files you are still having issues, please respond to this forum with an example region that you are trying to convert so that we can further assist you.

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.

Jairo Navarro 
UCSC Genomics Institute

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