search

Shicheng-Guo / rbiotools

Other
0 stars 0 forks source link

tabix vs bcftools view: 30 times faster #7

Open Shicheng-Guo opened 3 years ago

Shicheng-Guo commented 3 years ago 

(base) [sguo2@login02 gnomad2]$ time tabix gnomad.genomes.r2.1.1.sites.21.liftover_grch38.siteonly.vep.janssen.tab.gz chr21 | bgzip > chr21.vcf.tabix.gz

real    0m6.895s
user    0m9.100s
sys     0m0.664s

(base) [sguo2@login02 gnomad2]$ less -S chr21.vcf.tabix.gz
(base) [sguo2@login02 gnomad2]$ time bcftools view -r chr21 gnomad.genomes.r2.1.1.sites.21.liftover_grch38.siteonly.vep.janssen.tab.gz -Oz -o chr21.vcf.bcftools.gz
Failed to open gnomad.genomes.r2.1.1.sites.21.liftover_grch38.siteonly.vep.janssen.tab.gz: unknown file type

real    0m0.222s
user    0m0.002s
sys     0m0.004s