Vcftools Get-Info Output Name FORMAT

Question

[med_robles]

Hi all,

I am using the vcftools to extract data using a filter to exclude a list of snps: "list.txt".

e.g.

vcftools --vcf A.vcf --exclude-positions list.txt --out /home/new_vcfs/A-new

The file it creates is always called A-new.recode.vcf

Does anybody knows if there is any way of controlling the name of the output file to something like: A-new.vcf? I do not want a point and the word recode (.recode) in the name of my output file name. After doing this I will merge the vcf files (more than 20).

I really appreciate your help

Regards,
Meddly

Answer 1

[[e-mail]]

Hi Meddly,

How about writing to stdout and then redirecting to the filename of your choice?

vcftools --vcf A.vcf --exclude-positions list.txt --stdout > /home/new_vcfs/A-new.vcf