Question: Using vcfutils.pl command
0
gravatar for lcc1844
5.1 years ago by
lcc184430
United Kingdom
lcc184430 wrote:

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 • 11k views
ADD COMMENTlink modified 3.6 years ago by Biostar ♦♦ 20 • written 5.1 years ago by lcc184430

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

ADD REPLYlink written 5.1 years ago by iraun3.7k

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

ADD REPLYlink written 5.1 years ago by Pierre Lindenbaum127k

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 REPLYlink written 5.1 years ago by lcc184430

Have you followed these installation steps: http://vcftools.sourceforge.net/htslib.html?

ADD REPLYlink modified 5 months ago by RamRS26k • written 5.1 years ago by iraun3.7k
2
gravatar for lcc1844
5.1 years ago by
lcc184430
United Kingdom
lcc184430 wrote:

Thanks, I have done that and got

 /usr/share/samtools/vcfutils.pl

I don't know what share is though. 

ADD COMMENTlink written 5.1 years ago by lcc184430

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 REPLYlink written 5.1 years ago by iraun3.7k

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

ADD REPLYlink written 5.1 years ago by lcc184430

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.

ADD REPLYlink written 5.1 years ago by iraun3.7k
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