Access to the chain file (bosTau9ToBosTau6.over.chain.gz)

[Anton Shevlyakov]

Hello!

I am a masters student in Bioinformatics from Sirius University. For my genomics project I need to convert vcf files, created by ARS-USD1/2 (bosTau9) genome assembly, to vcf files, created by UMD_3.1 (bosTau6) genome assembly. Please, If possible, can you provide the bosTau9ToBosTau6.over.chain.gz file for my project?

Thank you in advance!

[Matthew Speir]

Hello, Anton. 

Thank you for your question about accessing LiftOver chain files.

These files can be found on our downloads server, https://hgdownload.soe.ucsc.edu/downloads.html. 

To access the LiftOver files for Cow/bosTau9, you would click "Mammals" at the top of the page, then select "Cow" from the now visible list of organisms. This will take you to a section with all of the Cow data. Under "Apr. 2018 (ARS-UCD1.2/bosTau9)," you should see a "LiftOver files" link. There you can find the LiftOver file that goes between bosTau9 and bosTau6: https://hgdownload.soe.ucsc.edu/goldenPath/bosTau9/liftOver/bosTau9ToBosTau6.over.chain.gz.

If you need the LiftOver file going in the opposite direction, so bosTau6 to bosTau9, then you can find that at the "LiftOver files" link under "Nov. 2009 (Bos_taurus_UMD_3.1/bosTau6)."

If there are any additional LiftOver files that you need that we don't provide, feel free to let us know and we can generate them.

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

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