Using vcfutils.pl command
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
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
blastn Command Not Found
written by 2Black_Cats •
-
seqtk-trinity error
written by fuad.fsu •
-
problem with Trinity command run in denovo transcriptome assembly
written by Aliviya •
-
picard error in trinty pipeline
written by eyonesi •
-
Error in bcftools view -bvcg command
written by hafiz.talhamalik
-
How can I edit the path to a new folder
written by mwanerhi erfgtr •
-
How to make bowtie available via PATH settings ?
written by iamtuttu5 •
-
How to set path of bowtie for trinity ?
written by iamtuttu5 •
-
Trinity Abundance estimation using RSEM
written by iamtuttu5 •
-
Reducing sequencing errors in .vcf file
written by lcc1844 •
Have you tried to type
locate vcfutils.plto see where the script is?I'm sure
:/bcftoolsis wrong. You didn't installbcftoolsin the 'root' directory.Hello and thank you - to install bcftools I did
Which required me to do
sudo apt-get installto 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/shareis 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/bindirectory. 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.