Re: [Vcftools-help] vcfidx files

[Anthony M. <ant...@ei...>]

Morty,

This is completely normal. Due to some of the changes we implemented in vcftools (specifically the ability to read in from streams), writing an index file is no longer necessary.

--
Anthony Marcketta
Bioinformatics Analyst
Department of Genetics
Albert Einstein College of Medicine
Van Etten B01
Bronx, New York 10461
________________________________________
From: Morty [mor...@fr...]
Sent: Wednesday, April 09, 2014 6:40 PM
To: vcf...@li...
Subject: [Vcftools-help] vcfidx files

One of the scientists I support at work requested that I upgrade
vcftools from 0.1.10 to 0.1.12a.  He has noted an issue that the new
version does not seem to generate .vcfidx files.  I can reproduce this
using one of the files from your examples:

vcftools --vcf valid-4.1.vcf --get-INFO ID

Using 0.1.10, this generates a .vcfidx file.  Using 0.1.12a, this does
not generate a .vcfidx file.

I looked through the announcements for the releases since 0.1.10 and
the vcftools-help mailing list archives, but do not see anything that
addresses this directly.  Is this difference normal?  I did see that
you removed --force-write-index in 0.1.12 -- was that because you
phased out the index?  Or do I have a broken installation?

The generated out.INFO file itself is identical.

Thanks!

- Morty

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