This is a test version of Biostars. For the public version, visit https://www.biostars.org.
tabix with specified coordinates

Hi!

I am using tabix to output from a vcf.gz file, some regions of interest. What is interesting is that when I specify, say,

10:7073963-7077040, I get results from regions outside of the range also. For example I get something at position 7073962. Why does tabix do this? Is this a bug? Or is this a built-in feature?

Please let me know.

Thank you.

tabix vcf
• 3,389 views • link
written by qmemcm • qmemcm

Is it a SNP that you're getting at 7073962 or a longer InDel? The latter would overlap your specified range.

• 0 views • link
written by Devon Ryan Devon Ryan

I don't think tabix looks at the bases when indexing. It only uses CHROM & POS.

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

True, you're probably correct then that this is a 0 vs. 1-based issue.

• 0 views • link
written by Devon Ryan Devon Ryan

It's not clear to me if tabix always uses a 0-based coordinate system.

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

1 answer

I think Devon's original answer is correct. I just gave that one example. But I have another: I specify the region as 721960-724370, and I get a long indel starting at 721929, which certainly overlaps my region.

Any more thoughts?

Thanks!

• 0 views • link
written by qmemcm • qmemcm

I should really refresh my memory of the tabix code, that'd answer this straight away. I know that there's code to deal with starts/ends, since a tabix index is basically an R-tree for block gzipped files. The question simply becomes whether the parser handles VCF files in an intelligent way or if it just blindly assigns start and and coordinates based on the same VCF column.

Edit: Note that if what I wrote above makes no sense to you that that's not something to worry about :)

• 0 views • link
written by Devon Ryan Devon Ryan

Log in to answer this question.

More posts like this