chain file request hg002

[Rob King]

Hi,

 

I’m enquiring if there is a chain file from grch38 to hg002 T2T v1.0.

I need to transfer a vcf file across and a chain file would make it easier.

 

Best wishes

Dr Robert King

 

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[Matthew Speir]

Hello, Rob.

Thank you for your chain file request for hg002.

First, could you provide the GCA accession for the specific version you are interested in? i.e. GCA_018852605.1/GCA_018852615.1 vs GCA_018852605.2/GCA_018852615.2.

Second, can you confirm that you want a lastz liftOver file? It will differ from the other HPRC liftOver files as our lastz/chains/nets pipeline is quite different from what the HPRC used to generate their files.

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Matthew Speir

UCSC Genome Browser, User Support

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[Rob King]

Hi Matthew,

 

I’m looking to move across a VCF file using https://gatk.broadinstitute.org/hc/en-us/articles/360037060932-LiftoverVcf-Picard and based upon http://genome.ucsc.edu/cgi-bin/hgLiftOver so whatever format the latter uses should be fine.

 

GCA_018852605.2/GCA_018852615.2 please

 

 

Best wishes

Rob

 

CONFIDENTIAL

[Rob King]

Hi Matthew,

 

I’ve got chain file from the T2T consortium so I’ll try that first, so please hold off.

I forgot going through my emails, they sent that email across to save you a job and then if it doesn’t work I may come back to you.

 

Best wishes

Rob

 

CONFIDENTIAL

From: Rob King
Sent: Monday, March 25, 2024 2:18 PM
To: Matthew Speir <msp...@ucsc.edu>
Cc: gen...@soe.ucsc.edu
Subject: RE: [genome] chain file request hg002

 

Hi Matthew,

 

I’m looking to move across a VCF file using https://gatk.broadinstitute.org/hc/en-us/articles/360037060932-LiftoverVcf-Picard and based upon http://genome.ucsc.edu/cgi-bin/hgLiftOver so whatever format the latter uses should be fine.

 

GCA_018852605.2/GCA_018852615.2 please

 

 

Best wishes

Rob

 

From: Matthew Speir <msp...@ucsc.edu>

[Maximilian Haeussler]

Hi Rob,

can you send us the URL to this chain file? We probably should add it.

thanks

Max

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[Rob King]

Hi Max,

 

See below what I received but I would check with Nancy Hansen that they can go up..it still may be beneficial for it to be done as per whatever method you use.

 

I’m hoping the experts there will create them, but if you’d like to give them a try, we have chain files that were created using the “nfLO” software here: https://github.com/evotools/nf-LO and using minimap2 the aligner. Here are links to them on aws:

https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/HG002/assemblies/changes/GRCh38_to_hg002v1.0.mat.chain.gz

https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/HG002/assemblies/changes/GRCh38_to_hg002v1.0.pat.chain.gz

https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/HG002/assemblies/changes/hg002v1.0_to_GRCh38.chain.gz

 

Coordinates in v1.0.1 are the same as v1.0, so the chain files above work with both of those releases.

 

Best wishes

Rob

 

CONFIDENTIAL