I am attempting to run the iHS tool from the GPAT++ suite. It requires the target individuals to be listed as a zero based, comma separated list. I would like to apply this to all individuals in the 1000 genomes phase 3 vcf files. My command is:
iHS --target <(seq -s ',' 0 2503) --file ../chr1.vcf.gz --region 1:860694-861694 --type GT
Here I am using a substitution in bash to create a comma separated sequence of all individuals. However, GPAT rejects this:
INFO: there are 1 individuals in the target INFO: target ids: /dev/fd/63 INFO: file: ../chr1.ancestral.vcf.gz INFO: set seqid region to : 1:860694-861694 FATAL: target option is required -- or -- less than two individuals in target
Is there a way of selecting all individuals? The
--target argument is required to run the program.
Just to confirm, I have tried running iHS with the argument
--target 0,1,2,3,4,5,6 just to confirm there are no other issues with my input, and this runs absolutely fine.