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Old 05-28-2019, 10:35 AM   #1
XeroxHero69
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Location: USA

Join Date: Apr 2019
Posts: 11
Default How to regenerate an index file for a gzipped vcf file?

I have a large vcf file with genomic data (330 GB) and an index file that accompanies it. I ran the command:

bcftools view -f PASS --threads 8 -r chr9:55252802-55252810 -o output.vcf.gz -O z 722g.990.SNP.INDEL.chrAll.vcf.gz

I get:

[W::hts_idx_load2] The index file is older than the data file: 722g.990.SNP.INDEL.chrAll.vcf.gz.tbi
[W::hts_idx_load2] The index file is older than the data file: 722g.990.SNP.INDEL.chrAll.vcf.gz.tbi


I was told that I need to regenerate my index file using Tabix. I have tried the following command that seemed to work for someone else having a similar problem:

tabix -p vcf 722g.990.SNP.INDEL.chrAll.vcf.gz

but it returned:

tbx_index_build failed: 722g.990.SNP.INDEL.chrAll.vcf.gz



I am not quite sure what command I should be using to regenerate my index file. Any help is greatly appreciated!
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