Chain File For HG18 to HG38 Conversion

[Stephen Tsou]

Hello,

I am trying to lift the ADNI data (HG18) to match the SNP 151 Common (HG38 I believe) so I can update the ADNI rsids and saw googling around that UCSC does have a chain file supposedly that convert between the two although a link does not exist on the liftover site.  

http://hgdownload-test.sdsc.edu/goldenPath/hg18/liftOver/hg18ToHg38.over.chain.gz

Is this true?  If so, how would I be able to access this chain file?  Thank you.  

best,

Stephen

[Luis Nassar]

Hello, Stephen.

Thank you for your interest in the Genome Browser.

The hg18 to hg38 chain file can be found here: https://hgdownload.soe.ucsc.edu/goldenPath/hg18/liftOver/hg18ToHg38.over.chain.gz

It looks like that link you have is an old URL to our development server. Did you find that referenced in some documentation or post online?

I am not familiar with the ADNI data, but if it is primarily/only SNPs or single variants and furthermore if they contain rsIDs, that would be a better way to lift the coordinates. See our FAQ on that here (https://genome.ucsc.edu/FAQ/FAQreleases.html#snpConversion).

I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.

Lou Nassar
UCSC Genomics Institute

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[Stephen Tsou]

Thank you so much Lou,

I will try the liftover software now.  Hopefully it goes smoothly.  

FYI, I got the link from this google conversation.  

https://groups.google.com/a/soe.ucsc.edu/g/genome/c/9O_hCdRliu4

[Stephen Tsou]

Hi Lou,

I am unsure of the documentation for bigBedNamedItems

How would I use that to lift?  It is unclear.  The .bb files only convert from hg19 to hg38 (not hg18).  I am also unsure of the arguments and unsure of the returned file even.  

best,

Stephen

[Gerardo Perez]

Hello, Stephen.

Thank you for your follow-up question.

Since the ADNI data seems to have rsIDs, the recommended method would be to use a list of rsIDs to convert the coordinates between assemblies. Since you want ADNI data (hg18) to match the SNP 151 Common (hg38), you can use the Table Browser. For example, if you have a list like the following:

rs73623060
rs6627577
rs1492296
rs1492295
rs5970267
rs12392070
rs35452540

You can then navigate to the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables) and make the following selections:
1.

clade: Mammal
genome: Human
assembly: Dec. 2013 (GRCh38/hg38)
group: Variation
track: Common SNPs(151)
table: snp151Common

2. Set the region to “genome”.
3. Click paste list next to “identifiers (names/accessions):” and enter your list of rsIDs. Then click submit. You may get a message of rsIDs having no match in the snp151Common table.
4. Set the output format to “Selected fields from primary and related tables”. This will allow you to select fields of interest.
5. Insert a name next to “output filename:”, such as rsIDs_snp151Common_hg38.
6. Click get output.
7. On the Select Fields from hg38.snp151Common page, select “chrom”, “chromStart”, “chromEnd”, and “name” fields. Click get output.
8. The output will give you the coordinates and the rsIDs for SNP 151 Common on hg38.

We do offer Common dbSNP(153) and Common dbSNP(155) on hg38, where the datasets are formatted as bigBed files instead of MariaDb tables. For these datasets, you could use the bigBedNamedItems command-line tool to extract the rsID coordinates, similar to the Table Browser steps. We updated our FAQ to make it more clear:
https://genome.ucsc.edu/FAQ/FAQreleases.html#snpConversion

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

To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CAF%3DP_nLpV0sQxwV5gUoC2WnEiWGKKrOD6gsgzOSPdiCPeRZ-uA%40mail.gmail.com.