<p>Hello,</p>

<p>A colleague pointed out this problem with GATK, which generates indexes in memory on the fly if it doesn't find those on disk:</p>

<pre>INFO  14:05:14,023 RMDTrackBuilder - Creating Tribble index in memory for file dbsnp_132.vcf
WARN  14:09:31,798 FSLockWithShared - WARNING: Unable to lock file dbsnp_132.vcf.idx (could not open read/write file channel)
WARN  14:09:31,798 RMDTrackBuilder - Unable to write to dbsnp_132.vcf.idx for the index file, creating index in memory only
</pre>

<p>I've read and gone through these two resources:</p>

<p><a href="http://www.broadinstitute.org/gsa/wiki/index.php/Tribble">http://www.broadinstitute.org/gsa/wiki/index.php/Tribble</a></p>

<p><a href="http://code.google.com/p/tribble/">http://code.google.com/p/tribble/</a></p>

<p>But I found it a bit awkward having to write my own java class just to generate an index file from a .vcf :-!</p>

<p>VCFTools does not seem to have that functionality either, at least according to their documentation:</p>

<p><a href="http://vcftools.sourceforge.net/docs.html">http://vcftools.sourceforge.net/docs.html</a></p>

<p>Anybody knows how to generate those .vcf.idx files in a more straightforward way ? </p>

<p>Thanks in advance !</p>

<p>PD: I just couldn't refrain myself from including this link too :)</p>

<p><a href="http://en.wikipedia.org/wiki/The_Trouble_With_Tribbles">http://en.wikipedia.org/wiki/The_Trouble_With_Tribbles</a></p>

<p>Hi
I found IGVTools, best for VCF indexing. </p>

<p>igvtools can be run from the command line or IGV itself (File&gt;Run igvtools...)  After launching, choose the Index command and browse to your .vcf file. The index file (.idx) will be created in the same directory as the .vcf file.</p>

<p>Thanks!
Jitendra</p>
