humanG1Kv37 or b37 to hg19 or hg38 chain files

Follow

Barton Prideaux

• September 07, 2022 19:40

Hi All,

Are there valid humanG1Kv37 or b37 to hg19 or hg38 chain files for the LiftoverVcf tool? 

It seems that this question as been addressed before but I haven't see a resolution:

https://gatk.broadinstitute.org/hc/en-us/community/posts/360067939931-humanG1Kv37-to-hg38-liftover-issues

https://gatk.broadinstitute.org/hc/en-us/community/posts/360077167731-humanG1Kv37-b37-to-hg38-liftover-issues

https://gatk.broadinstitute.org/hc/en-us/community/posts/360076074992-Converting-Reference-Genomes-from-b37-to-hg19

Here is a GATK team article discussing the discrepancies between assemblies.  This points you to the UCSC website for chain files.  

https://gatk.broadinstitute.org/hc/en-us/articles/360035890711-GRCh37-hg19-b37-humanG1Kv37-Human-Reference-Discrepancies

I have been unable to find them on the UCSC website and UCSC says this is a GATK responsibility:

https://groups.google.com/a/soe.ucsc.edu/g/genome/c/zYciCHx2PL8

There are some chain files available on the BroadGSA/GATK github but they are very old and I am unsure whether they are valid.

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

Here Pamela Bretscher says they are valid:

https://gatk.broadinstitute.org/hc/en-us/community/posts/4403222837787-Hi-Can-you-please-point-me-to-the-chain-file-for-human-g1k-v37-decoy-to-hg19-conversion?input_string=humanG1Kv37%20or%20B37%20to%20hg19%20or%20hg38%20chain%20files

Here Genevieve Brandt (she/her) says they are very old and should not be used:

https://gatk.broadinstitute.org/hc/en-us/community/posts/360074098891-Picard-liftover-error-Output-vcf-and-Reject-vcf-are-empty

 

Assistance would be very much appreciated!

 

Thanks,

Barton

 

0

• 

  Genevieve Brandt (she/her)

  • September 08, 2022 18:36

  Thank you for your post, Barton Prideaux! I want to let you know we have received your question. We'll get back to you if we have any updates or follow up questions. 

  Please see our Support Policy for more details about how we prioritize responding to questions. 

  0

  Comment actions Permalink

Please sign in to leave a comment.