Question: vcf not indexing
3
gravatar for alex
2.6 years ago by
alex160
United States
alex160 wrote:

Trying to index vcf file but getting the following

tabix -p vcf dbsnp_138.hg19.vcf.gz
Not a BGZF file: dbsnp_138.hg19.vcf.gz
tbx_index_build failed: dbsnp_138.hg19.vcf.gz

 

Thoughts on how to proceed?  Thanks!

tabix • 3.2k views
ADD COMMENTlink modified 2.6 years ago by Sean Davis23k • written 2.6 years ago by alex160
15
gravatar for Sean Davis
2.6 years ago by
Sean Davis23k
National Institutes of Health, Bethesda, MD
Sean Davis23k wrote:

Looks to me like the dbsnp file is not bgzipped?  

gunzip dbsnp_138.hg19.vcf.gz
bgzip dbsnp_138.hg19.vcf
tabix -p vcf dbsnp_138.hg19.vcf.gz
ADD COMMENTlink written 2.6 years ago by Sean Davis23k
1

@Sean Davis you just saved me a lot of frustration. I found this after a few searches and it worked. THanks

ADD REPLYlink written 6 months ago by jespinoz10
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