This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Extract the position from a huge vcf file

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 ?

vcf bcftools tabix
• 1,886 views • link
updated by Pierre Lindenbaum Pierre Lindenbaum • written by the_cowa • the_cowa

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

• 0 views • link
written by cpad0112 cpad0112

1 answer

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 ?)

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Log in to answer this question.

More posts like this