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LiftoverVCF chain file for b37 to hg38

For liftover of a b37 vcf to hg38, the gatk LiftoverVcf tool needs a chain file (b37Tohg38.chain). The documentation example uses this file but I don't see it in the GATK bundles. Is there one available? Or will the ucsc hg19Tohg38.chain file work despite the contig name difference?

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin
    edited August 2018

    @jfarrell
    Hi,

    I think you have to use the b37 to hg19 chain file, then use the hg19 to hg38 chain file. Unfortunately, there is no direct liftover chain file.

    -Sheila

  • jfarrelljfarrell Member ✭✭

    I have a hg19 to hg38 chain file. Is there a b37 to hg19 chain file available for download?

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @jfarrell
    Hi,

    Yes, we provide one in the resource bundle.

    -Sheila

  • marchoeppnermarchoeppner Kiel, GermanyMember
    edited October 2018

    Hi,
    just to clarify:

    I do not see any chain files in the bundle on the ftp server. There is a folder one level up called Liftover_chain_files. However, it does not contain any lift-over files to hg38 (neither for hg19 nor for b37).

    Where exactly are those hidden? ;)

    Cheers,
    Marc

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @marchoeppner

    Please see https://genome.ucsc.edu/goldenPath/help/chain.html for a description of chain files and http://hgdownload.soe.ucsc.edu/downloads.html#terms for where to download chain files.

    I hope this helps.

    Regards
    Bhanu

  • TabeaTabea GermanyMember

    Hi,
    I am experiencing a similar issue. I want to liftOver vcf files which are in "b37" to hg38. But I cannot find any chain file for b37? On the UCSC website there is only hg38 and hg19 available.
    And neither in the "Google Cloud Bucket" nor on your ftp server I can find any chain files.
    Could you please let me know me where I can find the chain files?
    Thanks a lot!

  • SChaluvadiSChaluvadi Member, Broadie, Moderator admin

    @Tabea
    I have tried to find this file for liftOver from b37 to hg19 in our FTP servers and was able to dig up this version but I am unsure of its integrity since it is from a few years ago. I also found that UCSC Genome Browser does not generate this liftOver from b37 to hg19. I do know that the difference between b37 and hg19 is the way that chromosomes are listed in the two and also that there are a few bases that are flipped between strands. Please read this forum post for more details on the difference between these two versions of the reference genome. Once you arrive at hg19, you can use the UCSC genome browser LiftOver file to convert to hg38. Please let me know if you need further help.

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