Entering edit mode
9.6 years ago
lcc1844
▴
40
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:
export PATH=$PATH:/bcftools
$ echo $PATH
/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/bcftools
If I try to repeat the filtering command using this, I get the same error:
bcftools view my.var.bcf | /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/bcftools:/vcfutils.pl varFilter - > my.var-final.vcf
I can understand that the vcfutils.pl file is not being found but I am stuck trying to work out how to fix this. I'm sure it must be something very basic but I'm struggling anyway!
Any advice would be much appreciated.
Thanks
Have you tried to type
locate vcfutils.pl
to see where the script is?I'm sure
:/bcftools
is wrong. You didn't installbcftools
in the 'root' directory.Hello and thank you - to install bcftools I did
Which required me to do
sudo apt-get install
to install it. But I don't know where it has installed!Have you followed these installation steps?
Thanks, I have done that and got
I don't know what share is though.
The "share" word is used because what is under
/usr/share
is platform independent, and can be shared among several machines across a network filesystem. Therefore this is the place for manuals, documentations, examples etc.Hi, thanks again. How can I move bcftools to an appropriate place?
You should move to
/usr/bin
directory. This folder is the directory for the executables that are accessed by all users (everybody have this directory in their$PATH
). So, you maybe want to copy/move bcftools executables to this folder.