Request for Guidance on GRCh38 to T2T-CHM13v2.0 LiftOver Chain File for Batch Conversion

[Praveen Kumar, Sanjana Devi]

Dear UCSC Genome Browser Support Team,

I hope this message finds you well. I am working on a project that involves the conversion of a large batch of genomic data files from GRCh37 to GRCh38 and then from GRCh38 to T2T-CHM13 v2.0.

I have successfully found the necessary chain file to convert from GRCh37 to GRCh38, but I am currently unable to locate a GRCh38 to T2T-CHM13 v2.0 chain file in the UCSC archives or elsewhere. Given the large number of files (I can't submit each file individually through the website for conversion, as I need to process a large number of files in a batch), I am looking for guidance on how to proceed. Could you kindly provide assistance with the following:

1. Is there a GRCh38 to T2T-CHM13 v2.0 chain file available for download? If so, could you please share the link?
2. If this chain file is not available, could you recommend alternative approaches or tools for generating the required chain file for my batch conversion?
3. Are there any resources or documentation available that could help in the conversion process from GRCh38 to T2T-CHM13 v2.0?

Thank you in advance for your time and assistance.

Best regards,
Sanjana

[Luis Nassar]

Hi, Sanjana.

Our abbreviation for T2T-CHM13 is 'hs1' (https://hgdownload.soe.ucsc.edu/downloads.html). You can find the chain file for hg38 to T2T in the liftOver download directory:

https://hgdownload.soe.ucsc.edu/goldenPath/hg38/liftOver/hg38ToHs1.over.chain.gz

I am not aware of any additional recommendations for lifting between those two assemblies, however, if you have specific questions about variants that did not lift as expected, then we can take a look at those individual cases.

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Lou Nassar
UCSC Genomics Institute

[Praveen Kumar, Sanjana Devi]

Thank you so much.

Regards,

Sanjana