Using vcfutils.pl command

Question

[lcc1844]

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

[iraun]

Have you tried to type locate vcfutils.pl to see where the script is?

[Pierre Lindenbaum]

I'm sure :/bcftools is wrong. You didn't install bcftools in the 'root' directory.

[lcc1844]

Hello and thank you - to install bcftools I did

git clone --branch=develop git://github.com/samtools/bcftools.git

Which required me to do sudo apt-get install to install it. But I don't know where it has installed!

[iraun]

Have you followed these installation steps?

[lcc1844]

Thanks, I have done that and got

/usr/share/samtools/vcfutils.pl

I don't know what share is though.

[iraun]

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.

[lcc1844]

Hi, thanks again. How can I move bcftools to an appropriate place?

[iraun]

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.