Need help to LiftOver file

[Priyatama Pandey]

Hi,

I work on somatic variant using whole exome sequencing. I follow GATK best practices pipeline which says for short variant discovery in exome and other targeted sequencing: b37/hg19. So I am using human assembly “human_g1k_v37_decoy”. Now I want to liftover my variants VCF file  on hg19.

I looked the link  http://hgdownload.cse.ucsc.edu/goldenPath/hg38/liftOver/ . But I am basically looking for b37ToHg19.over.chain.gz file.

Actually, we are interested to know even the minor difference in the coordinates of hg19 and b37.

 

I really appreciate any help regarding this.

 

Best,

Priya

 

Keck School of Medicine

University of Southern California

 

 

 

[Cath Tyner]

Hello Priya,

Thank you for contacting the UCSC Genome Browser support forum regarding the location of a chain file for b37-hg19. In short, you will need to contact GATK for assistance, UCSC does not generate this chain file. I found some related urls (below) that may help you, but ultimately it looks like you will need to ask GATK at their support forum.

Note #4 here:

https://software.broadinstitute.org/gatk/documentation/article.php?id=1213

An FTP location is given for the chain file in this forum thread, but the FTP link is broken. It appears that GATK may have recently re-arranged their FTP site, which may explain why the file location has moved. 

Here is a related question on the GATK forum:

Can you help me to understand the difference between b37 and hg19 resource bundles?

 

The two versions of the reference genomes are not exactly the same. There are a few differences, for example some bases that are flipped between strands. That is why we have liftover chain files to convert between the two versions. So there may be a few variants that are filtered out in one version relative to the other. But this should affect only a tiny proportion of variants.

You are also welcome to search the UCSC Genome Browser support forum. For example, you can search "hg19 b37" to see previously answered related mailing list questions from our support forum. For example: https://groups.google.com/a/soe.ucsc.edu/forum/#!topic/genome/o6Nue3ggh2I

Finally, I found a b37tohg19.chain file by doing a google search for "b37tohg19 chain file", but I do not know anything about the integrity of this file. It does appear to be on the official repository:

https://github.com/broadgsa/gatk

"GATK Official Release Repository: contains the core MIT-licensed GATK framework, free for all uses."

https://github.com/broadgsa/gatk/tree/master/public/chainFiles

https://github.com/broadgsa/gatk/blob/master/public/chainFiles/b37tohg19.chain

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Cath Tyner

UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute

UCSC Genome Browser

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[Priyatama Pandey]

Thankyou Cath for your respond.

I appreciate your help. Github link helped me. I have gone through  GATK forum and found many link to download the chain files but all are broken. 
Have a great weekend.

Best,

Priya

_____________________________
From: Cath Tyner <ca...@ucsc.edu>
Sent: Thursday, March 23, 2017 5:41 PM
Subject: Re: [genome] Need help to LiftOver file
To: Priyatama Pandey <priy...@usc.edu>
Cc: <gen...@soe.ucsc.edu>

Hello Priya,

Thank you for contacting the UCSC Genome Browser support forum regarding the location of a chain file for b37-hg19. In short, you will need to contact GATK for assistance, UCSC does not generate this chain file. I found some related urls (below) that may help you, but ultimately it looks like you will need to askGATK at their support forum.

Note #4 here:

https://software.broadinstitute.org/gatk/documentation/article.php?id=1213

An FTP location is given for the chain filein this forum thread, but the FTP link is broken. It appears that GATK may have recently re-arranged their FTP site, which may explain why the file location has moved. 

Here is arelated question on the GATK forum:

Can you help me to understand the difference between b37 and hg19 resource bundles?

 

The two versions of the reference genomes are not exactly the same. There are a few differences, for example some bases that are flipped between strands. That is why we have liftover chain files to convert between the two versions. So there may be a few variants that are filtered out in one version relative to the other. But this should affect only a tiny proportion of variants.

You are also welcome to search theUCSC Genome Browser support forum. For example, you can search "hg19 b37" to see previously answered related mailing list questions from our support forum. For example:https://groups.google.com/a/soe.ucsc.edu/forum/#!topic/genome/o6Nue3ggh2I