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ikalatskaya / ISOWN

Apache License 2.0
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Issue about different reference human assemblies #27

Open anyone1985 opened 5 years ago

anyone1985 commented 5 years ago

Hi,

I'm new for this wonderful tool. When i look up the 00-All.vcf.gz, I think it uses GRCh38.p7 as the reference assembly. While the other databases use Hg19 as the reference. I'd like to know if it is right to use liftover utility to convert genome coordinates from GRCh38 to Hg19.

Flope commented 3 years ago

I also noticed the inconsistency of the data coordinates in the instructions. You can get on those DBs the hg19 version of them. For the, dbSNP wget https://ftp.ncbi.nih.gov/snp/organisms/human_9606_b151_GRCh37p13/VCF/00-All.vcf.gz --no-passive-ftp

And the ExAC dataset should be this one: wget https://storage.googleapis.com/gcp-public-data--gnomad/legacy/exac_browser/ExAC.r1.sites.vep.vcf.gz