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Missing variants in hg38 lift-over of 1000-genomes data

Hi everyone,

I've been looking in the hg38 mapped version of chromosome 12 from 1000 genomes (phase 3) data. Curiously, at certain parts (longer than several hundred kb) of this lift-over version, there are not any SNPs. The region I'm interested in is chromosome 12: 7,500,000-8,000,000. When I run the following command, I simply don't get any SNPs, but the header:

tabix -h ALL.chr12_GRCh38.genotypes.20170504.vcf.gz 12:7500000-8000000

Whereas, when I use the same command for most other parts of the vcf, I can get the SNP list normally.

So, I was wondering if it's somehow a known issue or am I doing something wrong as usual.

Any help is much appreciated.

Cheers, Gökberk

1000genomes vcf
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written by gokberk gokberk

1 answer

Direct hg38 calls are available here. Have you checked into those?

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written by GenoMax GenoMax

Oh, didn't know that direct hg38 calls were available. It looks like they have all SNPs that were missing in the lift-over indeed. Thanks a lot genomax!

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written by gokberk gokberk

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