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Is there any way to make samtools tabix go faster?

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.

tabix vcf bcf samtools
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written by curious curious

1 answer

I don't think tabix is able to work with bcf files (?)

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written by Pierre Lindenbaum Pierre Lindenbaum

Hmm. When I go tabix my_fav.bcf I get a my_fav.bcf.csi. Then I am able to use bcftools 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

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written by curious curious

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