Extract the position from a huge vcf file

Question

[the_cowa]

I have a list with chromosome and the position as like this

 Chr1 254
 Chr5 8965
 ChrX 25
 ChrY 8965
 Chr19 2354

and need to extract the position from a huge vcf file of size 1 TB. So far I have used

bcftools view -T Locations.txt Input.vcf.gz >Output.vcf

But it is taking days to finish. Is there any method/programme to speed up the run OR is it possible to run with tabix ?

[cpad0112]

Try tabix. bgzip the vcf, index the vcf and try tabix -R with the input OP list.

Answer 1

[Pierre Lindenbaum]

use option -R , not option -T

-R, --regions-file <file>           restrict to regions listed in a file
-T, --targets-file [^]<file>        similar to -R but streams rather than index-jumps. Exclude regions with "^" prefix

furthermore your input file is not a BED file (chrom start end). I'm not sure it will work. (May be ?)