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