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marbl / CHM13

The complete sequence of a human genome
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chain file to liftover v1.1 to hg38 #29

Closed pushpinder11 closed 3 years ago

pushpinder11 commented 3 years ago

Is there a chain file available to perform a life over from v1.1 to hg38?

skoren commented 3 years ago

The UCSC browser provides chains between v1.0 and hg38 (http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=1128870359_RtudPntcUkokyX1DcrCMmfDWkfXd&db=hub_2395475_t2t-chm13-v1.0&c=chr10&g=hub_2395475_grch38Lastz). I also added links to them from this GitHub page. There are also chain files to liftover between v1.0 and v1.1. You should be able to do a two-step liftover (e.g. hg38->v1.0->v1.1) to go between hg38 and v1.1 using those.

slw287r commented 2 years ago

FYI: Chains between v1.1 and hg38 grch38.t2t-chm13-v1.1.over.chain t2t-chm13-v1.1.grch38.over.chain

bw2 commented 2 years ago

Thanks. I've added them to https://liftover.broadinstitute.org/

lubertorubior commented 2 years ago

Hello, thanks for sharing the chain files. Which should be the proper hg38 fasta file to use tools such as Picard's LiftoverVcf with these chain files?

Thanks.

ebioman commented 11 months ago

Hi Thanks for the chain files, is there by chance anywhere described how they have been generated ? Cheers