Issue with tabix - Could not load .tbi index

[cr234]

I've been trying to generate vcf.gz files and associated .vcf.gz.tbi indexes for multiple .vcf files simultaneously. I first ran into the problem of bgzip only creating one .vcf.gz file when I ran;

bgzip *.vcf

However I got round this by running the command several (400) times;

n=0; while [[ $n -lt 400 ]]; do bgzip -i *.vcf; n=$((n+1)); done

I wanted to do the same for tabix so tried to use;

n=0; while [[ $n -lt 400 ]]; do tabix -p vcf *.vcf.gz; n=$((n+1)); done

However this gives me the error;

'Could not load .tbi index of file1.vcf.gz'

This is the first file in the list. Tabix works just fine if I use;

tabix -p vcf file1.vcf.gz

However I don't want to have to type out ~400 odd .vcf.gz file names. Does anyone know why I am having this issue?

Thanks.

[GenoMax]

How about:

for f in *.vcf.gz
do[INDENT]tabix -p vcf $f[/INDENT]
done

as a one liner

for f in *.vcf.gz; do tabix -p vcf $f; done

[cr234]

Yep that works great, thanks a lot!