Using vcfutils.pl command
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Entering edit mode
6.2 years ago
lcc1844 ▴ 30

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 alignment • 13k views ADD COMMENT 0 Entering edit mode Have you tried to type locate vcfutils.pl to see where the script is? ADD REPLY 0 Entering edit mode i'm sure :/bcftools is wrong. You didn't install /bcftools in the 'root' directory. ADD REPLY 0 Entering edit mode 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!  ADD REPLY 0 Entering edit mode Have you followed these installation steps: http://vcftools.sourceforge.net/htslib.html? ADD REPLY 2 Entering edit mode 6.2 years ago lcc1844 ▴ 30 Thanks, I have done that and got /usr/share/samtools/vcfutils.pl I don't know what share is though. ADD COMMENT 0 Entering edit mode 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. ADD REPLY 0 Entering edit mode Hi, thanks again. How can I move bcftools to an appropriate place? ADD REPLY 0 Entering edit mode 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.