Missing .vcf.gz.tbi produces misleading error

[adamnovak]

If you try to do vg construct with a .vcf.gz file that has no associated .tbi, you get this message:

[tabix++] the index file is older than the vcf file. Please use '-f' to overwrite or reindex.

The message is doubly wrong: there's no older index file around (it's just absent) and there's no -f option that can be used to solve the problem.

The message should be replaced with a more informative one telling the user to index the file.

[verne91]

I come across this problem. So how can I deal with it?

[adamnovak]

@verne91 The way to actually solve the problem is to delete the old index with rm whatever.vcf.gz.tbi and then use tabix -p vcf whatever.vcf.gz to regenerate it from the vcf.

If you're absolutely positive the index corresponds to the vcf (and you just downloaded them in the wrong order or something) you can use touch whatever.vcf.gz.tbi to make the tabix file look newer than the vcf, without rebuilding it.

[verne91]

Yes. "touch" helps!