Vcftools Get-Info Output Name

Question

[mark.dunning]

Hi all,

I am using the vcftools to extract data from a VCF file into tabular form, so that I can read into R and do some computations and visualisation

e.g.

vcftools --vcf sample1.vcf --get-INFO MQ --get-INFO MQ0

The file it creates is always called out.INFO. Is there really no way of controlling the name of the output file to something like sample1.INFO? If I want to extract info from several vcfs in the same directory, they will overwrite each other.

Regards,

Mark

Answer 1

[Matt Shirley]

Based on the documentation, I think you are able to specify something like this:

vcftools --vcf sample1.vcf --get-INFO MQ --get-INFO MQ0 --out sample1

You can write a shell script that will set the --out prefix based on the input filename. If you need help with this, just ask.

[mark.dunning]

Brilliant, just what I was looking for...Should have read the documentation in a bit more detail first though :/