Re: [genome] Digest for genome@soe.ucsc.edu - 1 update in 1 topic

[Minou Bina]

Hello,

I’m having trouble with ClinVar track on hg19

It’s like now you see it, then you don’t. It’s very important that I could see the very nucleotide repeats 

Best,

Minou Bina

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• GRCz12 liftover - 1 Update

GRCz12 liftover

Clay Fischer <clayf...@ucsc.edu>: May 14 10:20AM -0700 Hi Angela,   Our engineer has completed the generation of these files, thanks for your patience. https://hgdownload.soe.ucsc.edu/hubs/GCA/052/040/795/GCA_052040795.1/liftOver/GCA_052040795.1ToDanRer11.over.chain.gz https://hgdownload.soe.ucsc.edu/goldenPath/danRer11/liftOver/danRer11ToGCA_052040795.1.over.chain.gz   Thanks, Clay Fischer UCSC Genomics Institute     On Mon, Apr 27, 2026 at 3:00 AM Angela Bekesi <angela...@gmail.com> wrote:

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[Gerardo Perez]

Hello Minou,

As my colleague Lou mentioned in the other email, the variants are missing because ClinVar deleted them.

If you would like to view those variants, you can load one of our archived ClinVar bigBed files as a custom track. The archive directory is here: https://hgdownload.soe.ucsc.edu/goldenPath/archive/hg19/clinvar/

The most recent version that still contains all of those variants is 2025-12-08. To load it, go to "My Data > Custom Tracks > Add Custom Tracks" and paste this single line:

track type=bigBed name="ClinVar 2025-12-08" visibility=pack bigDataUrl=https://hgdownload.soe.ucsc.edu/goldenPath/archive/hg19/clinvar/2025-12-08/clinvarMain.bb

Please note that in the custom track, the variants will be labeled by their ClinVar accession (for example, VCV000363420) rather than by the variant change (G>A, del, insGGCAGC, etc.) that the ClinVar track shows. You can click on any item to see the full variant details.

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.

Gerardo Perez
UCSC Genomics Institute

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[Minou Bina]

Thank you. I found in the track SNPs. actually,  I was going about contacting you about this set of SNPs. I think they are very very important. If you go to examine CHD7 exon 1, you could find them. Minou 

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From: Gerardo Perez <gpe...@ucsc.edu>
Sent: Thursday, May 21, 2026 5:59:11 PM
To: Minou Bina <bi...@purdue.edu>
Cc: gen...@soe.ucsc.edu <gen...@soe.ucsc.edu>
Subject: Re: [genome] Digest for gen...@soe.ucsc.edu - 1 update in 1 topic

 

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