Entering edit mode
4.5 years ago
curious
▴
820
I am tab indexing a pretty big bcf of a single chromosome with tabix, which takes about 8 or so hours like this:
$tabix my_fav.bcf
I have tried googling to see if there is anyway to make it go faster, but at least to my eyes I don't see an arg that can be tweaked to make this go faster:
http://www.htslib.org/doc/tabix.html
Am I missing any tricks to make tabix run faster or in a multithreading mode? Or an alternative to tabix that gets the same results faster? Any advice is greatly appreciated.
Hmm. When I go
tabix my_fav.bcf
I get amy_fav.bcf.csi
. Then I am able to usebcftools view -R
just like I would with the.tbi
file generated from a vcf. I guess I thought.csi
was just the bcf counterpart.Oh no...
I think I might have just answered my own question and the faster alternative to tabix might be to use:
bcftools index --threads 64 my_fav.bcf