Question regarding Liftover error fixing (GRCh38 conversion to GRCh37)

[Olivia Cao]

Hello,

Hope you are having a lovely day, I encountered several error messages when attempting to transfer a set of SNPs from GRCh38 to GRCh37. Here is a screenshot of the reported error, there are mainly three types of errors reported:

1. split in new;

2. deleted in new;

3. partially deleted in new.

 

I found a post with a solution to a similar problem (https://groups.google.com/a/soe.ucsc.edu/g/genome/c/egfMAIRfQBQ). However, our team is trying to keep the integrity of original data and convert the assembly without splitting one SNP into multiple new ones. If you would be so kind to help, the parameters are attached in a screenshot and reported error in the text file.

Hope you have a wonderful rest of today.

Best wishes,

Olivia

[Jairo Navarro Gonzalez]

Hello,

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

We do not recommend using the LiftOver tool to lift the SNPs from hg38 to hg19. Lifting a single base between assemblies is not always a trivial task as it may not get a high enough score to be considered a successful conversion.

If you have the rsIDs for all of your SNPs, we recommend pulling the hg19 coordinates from the dbSNP 153 track by searching for the rsID on hg19 or using the Table Browser. If you are unfamiliar with using the Table Browser to retrieve SNPs from the dbSNP 153 track, you can get more information from the following help page:

https://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#BatchQuery

If you wish to use the LiftOver tool, then you will have to add some bases upstream and downstream of the SNP location. However, if you choose this approach, we recommend using the LiftOver & ReMap track to look at the chains in those regions to see where they map between assemblies. You could also try to BLAT the surrounding sequence to see if there are multiple matches in hg19.

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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