GRCh37.p13?

[Ben Keller]

Can you confirm that hg19/Ch37 includes patches from July 2013 (GRCh37.p13)?  It looks like it, but I don’t want to assume.

Also, I want to liftover Ch37 (circa 2009) positions to Ch37.p13 positions — is this possible?

Thanks,

Ben
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Ben Keller

bjke...@vt.edu

[Matthew Speir]

Hello Ben,

Thank you for your question about GRC patch releases in the UCSC Genome Browser. The Genome Reference Consortium (GRC) defines patches as small updates to regions of the genome sequence that are released outside of their standard release cycle. These patches allow the GRC to provide updated information about certain regions of the genome, without having to change the coordinates for entire chromosomes. You can find more information on how the GRC define and handle patches here: https://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/info/patches.shtml.

For GRCh37/hg19 Patch 10, we created a track that contained the patch sequences mapped to the reference sequence, http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=altSeqComposite10. We have not created a similar track for Patch 13. You may be interested in using the newest human assembly, GRCh38/hg38, which contains all of the GRCh37 patch sequences incorporated into the reference genome. You can lift your annotations from GRCh37/hg19 assembly to the GRCh38/hg38 assembly using the LiftOver tool, http://genome.ucsc.edu/cgi-bin/hgLiftOver.

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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