A colleague pointed out this problem with GATK, which generates indexes in memory on the fly if it doesn't find those on disk:
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
I've read and gone through these two resources:
But I found it a bit awkward having to write my own java class just to generate an index file from a .vcf :-!
VCFTools does not seem to have that functionality either, at least according to their documentation:
Anybody knows how to generate those .vcf.idx files in a more straightforward way ?
Thanks in advance !
PD: I just couldn't refrain myself from including this link too :)