Liftover alternate haplotype hGRCh38

[Monique Van Veghel - Plandsoen]

Dear Sir/Madame,

 

Is there a liftover file available which can liftover GRCh38 _alt contigs to the main contig on the same build?

For example I want to know the main genomic positions for: chr2_KI270773v1_alt     4167      64734   SNTG2_1:NM_018968.4_1

 

 

 

What is the best way to perform this (for a list of 700 contigs)?

 

Best Regards,   Ing M.M. Van Veghel - Plandsoen Bioinformatician Clinical Genetics   m.pla...@erasmusmc.nl

 

[Jairo Navarro Gonzalez]

Hello,

Thank you for using the UCSC Genome Browser and sending your inquiry.

You could use multi-region mode to view the alternate haplotypes alongside the main chromosomes on the UCSC Genome Browser. Using this feature, you can visualize the flanking regions around the _alt or _fix chromosome.

You can learn more about this feature from the following help page:

https://genome.ucsc.edu/goldenPath/help/multiRegionHelp.html#Example5

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.

Jairo Navarro
UCSC Genome Browser

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[Jairo Navarro Gonzalez]

Hello again,

You may also be interested in the GRC Incident track for hg38, which shows assembly problems that have been noted or resolved, as reported by the Genome Reference Consortium (GRC).

https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&c=chr7&g=grcIncidentDb

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.
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Jairo Navarro
UCSC Genome Browser

[Monique Van Veghel - Plandsoen]

Hello Jairo,

 

Thank you for your response.

But I’m not looking for a UCSC track to make the contigs visible on the main contig. But I’m looking for a way to extract the genomic positions of the main contig belonging to a given alt contig.

I didn’t explain it clear I suppose but for example:

 

I have (let’s say) 100 reads on “chr2_KI270773v1_alt      4167              64734   SNTG2_1:NM_018968.4_1”. This _alt contig covers (part of) genes SNTG2. I want to count how many reads are on the corresponding genomic positions of the main contig and add them together.

So I want to find  for the _alt positions (4167 - 64734) the exact corresponding genomic positions of SNTG2. (And that for around 700 contigs).

Is there a download file available to support me with that?

 

Best regards,

Ing M.M. Van Veghel - Plandsoen

Bioinformaticus Klinische Genetica

 

From: Jairo Navarro Gonzalez <jnav...@ucsc.edu>
Sent: Wednesday, May 28, 2025 21:17
To: Monique Van Veghel - Plandsoen <m.pla...@erasmusmc.nl>
Cc: gen...@soe.ucsc.edu
Subject: Re: [genome] Liftover alternate haplotype hGRCh38

 

 

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[Jairo Navarro Gonzalez]

Hello,

Thank you for using the UCSC Genome Browser and sending your follow-up inquiry.

We have an "analysis set" that deliberately excludes the _alt and _fix sequences. It may be best for you to rerun your alignments with the analysis set to obtain the per-chromosome alignments.

https://hgdownload.gi.ucsc.edu/goldenPath/hg38/bigZips/analysisSet/

If this is not what you want, please send us an example sequence to help us gain a better understanding of what you are trying to achieve.

I look forward to your reply. 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.

Jairo Navarro
UCSC Genome Browser