About the liftover chain file for new Bovine Genome (ARS-UCD1.3)

[Cheng-En Tan]

Hi,

I am ChengEn, a computer science PhD student at UC Davis.

I would like to liftover the vcf files from UMD3.1.1 to ARS-UCD1.3. I saw there is available data for conversion to ARS-UCD1.2, but a newer version (ARS-UCD1.3) is published and I would like to convert to a newer version.

I saw there is a description for building the chain file, but I would like to ask whether you already have the chain file (for ARS-UCD1.3) already.

Thank you,

Sincerely,

ChengEn

[Cheng-En Tan]

Hi UCSC Genome Browser HelpDesk, 

I am ChengEn, a computer science PhD student at UC Davis.

I would like to liftover the vcf files from UMD3.1.1 to ARS-UCD1.3. I saw there is available data for conversion to ARS-UCD1.2, but a newer version (ARS-UCD1.3) is published and I would like to convert to a newer version.

I saw there is a description for building the chain file, however, there are technical issues that I cannot follow the instructions: Lots of the path in the scripts are fixed, especially the parallel platform (parasol). I tried to install and configure the parasol platform for building the chain file yesterday on more than one computer for no less than eight hours, but I still cannot make the platform work.

I would like to ask whether you already have the chain file (for ARS-UCD1.3) already, or whether there is a server open to the public for building the chain files for liftover.

Thank you,

Sincerely,

ChengEn

[Matthew Speir]

Hello, ChengEn. 

Thank you for your question about LiftOver files. 

Here are the details for the two assemblies:
GCF_002263795.3_ARS-UCD2.0 cattle (Hereford L1 Dominette 01449 42190680 v2.0 2023 USDA)
GCF_000003055.6_Bos_taurus_UMD_3.1.1 cattle (Hereford UMD_3.1.1 2014)

The LiftOver files are available here:
https://hgdownload.soe.ucsc.edu/hubs/GCF/002/263/795/GCF_002263795.3/liftOver/GCF_002263795.3ToGCF_000003055.6.over.chain.gz
https://hgdownload.soe.ucsc.edu/hubs/GCF/000/003/055/GCF_000003055.6/liftOver/GCF_000003055.6ToGCF_002263795.3.over.chain.gz

And you can view these genomes and the chain tracks (that display these alignments) here:
https://genome.ucsc.edu/h/GCF_002263795.3
https://genome.ucsc.edu/h/GCF_000003055.6

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.

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Matthew Speir

UCSC Genome Browser, User Support

UC Santa Cruz Genomics Institute

Revealing life’s code.

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