chain file GRCh37.p10 to GRCh38 (primary assembly)

[Mark Wagoner]

Hello,

We are in the process of updating to the GRCh38 primary assembly from 23andMe's annotation version 104 (GRCh37.p10).

However the CrossMap software appears not to have a chain file to faciliate this conversion. 

Would it be possible for you all to create a chain file to update from GRCh37.p10 to the GRCh38 primary assembly (no patches)?

Thank you,

Mark Wagoner

Co-founder, NutraHacker, LLC

[Luis Nassar]

Hello Mark,

Thank you for your interest in the Genome Browser and for your question regarding chain files.

We do not usually create chain files between patch sequences (fix/alt - https://genome.ucsc.edu/FAQ/FAQdownloads.html#downloadAlt) and other assemblies. As the sequence in all the main chromosomes of GRCh37 are the same as GRCh37.p10, the hg19ToHg38 chain file is sufficient for most users. If this works for your purposes, the hg19ToHg38 chain file can be found on our download server: http://hgdownload.soe.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz

If, however, you have annotations on fix/alt sequences introduced in one of the GRCh37/hg19 patches that you would like to convert to GRCh37/hg38, you would need a different chain file. Users can generate their own chain files directly by following our help pages, though it is not a trivial undertaking (http://genomewiki.ucsc.edu/index.php/DoSameSpeciesLiftOver.pl). If you decide to create new chain files, I would also encourage you to search our mailing list for similar cases: https://groups.google.com/a/soe.ucsc.edu/forum/#!searchin/genome/

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.

Lou Nassar
UCSC Genomics Institute

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