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macarthur-lab / gnomad_browser

gnomAD browser pre-ASHG 2018
MIT License
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Chr1 VCF truncated in liftover_grch38 #110

Closed donnawerling closed 6 years ago

donnawerling commented 6 years ago

Lifted-over chromosome 1 VCF file at gs://gnomad-public/release/2.0.2/vcf/genomes/liftover_grch38/ appears to be truncated. Running bcftools view or other bcftools command returns the following warning: "[W::bgzf_read_block] EOF marker is absent. The input is probably truncated"

File size supports this, as the chromosome 1 file is far smaller than chromosome 2, etc. Possible problem with liftover, or data upload?

bw2 commented 6 years ago

Thanks for reporting this. Indeed, the liftover job didn't complete. I thought I checked this, but somehow missed chr1. I'll be re-uploading the chr1 file after liftover finishes running. (Also, I've double-checked that the other chromosomes don't have this issue)

bw2 commented 6 years ago

I've updated the chr1 vcf, tbi and log files.

For example, this should work now:

tabix http://storage.googleapis.com/gnomad-public/release/2.0.2/vcf/genomes/liftover_grch38/gnomad.genomes.r2.0.2.sites.chr1.liftover.b38.vcf.gz 1:12345-54321 | wc -l