GATK liftOver chain file for human_g1k

GATK liftOver chain file for human_g1k_v37.fasta

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3.9 years ago

brismiller ▴ 50

Hey all, is there a chain file that I can use to lift over variants from human_g1k_v37.fasta to hg38?

I ran GATK's LiftoverVcf using the hg19ToHg38.over.chain file and it worked for most of the variants in the test files that I ran it on. ~99.93%, but I was just wondering if anyone knew of a specific chain file that I could use.

Here is a description of g1k_v37, from my understanding it is a branch off of b37, which is a branch off of hg19. https://gatk.broadinstitute.org/hc/en-us/articles/360035890711-GRCh37-hg19-b37-humanG1Kv37-Human-Reference-Discrepancies#b37

gatk genome sequencing alignment • 2.5k views

ADD COMMENT • link updated 3.7 years ago by Biostar 20 • written 3.9 years ago by brismiller ▴ 50

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In case nobody answers, you may receive a better response on the GATK support forum. Link back here if possible.

ADD REPLY • link 3.9 years ago by Kevin Blighe 87k

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i just made a gatk post https://gatk.broadinstitute.org/hc/en-us/community/posts/360067939931-b37-to-hg38-liftover-issues I will keep this post updated as things progress

ADD REPLY • link 3.9 years ago by brismiller ▴ 50

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In the end I was unable to find a better chain file(s) for this conversion. But, if you stop and think about it, if your variants you are interested in are in protein coding regions (like mine are) then this should not affect your results as the g1k_v37 -> b37 -> hg19 conversion mainly affects the alternative contigs (at least from my understanding).