I am trying to do some variant filtering via samtools and have made a var.bcf file.
When I try the following I get the error 'No such file or directory'.
bcftools view my.var.bcf | vcfutils.pl varFilter - > my.var-final.vcf
In my Samtools folder I can't actually see bcftools or vcfutils.pl anywhere but I can do this:
$ echo $PATH
If I try to repeat the filtering command using this, I get the same error:
bcftools view my.var.bcf | /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/bcftools:/vcfutils.pl varFilter - > my.var-final.vcf
I can understand that the vcfutils.pl file is not being found but I am stuck trying to work out how to fix this. I'm sure it must be something very basic but I'm struggling anyway!
Any advice would be much appreciated.