Difference between revisions of "VCFTools"
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== Introduction == | == Introduction == | ||
VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files. | VCFtools is a program package designed for working with VCF files, such as those generated by the [http://www.1000genomes.org/ 1000 Genomes Project]. The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files. | ||
This toolset can be used to perform the following operations on VCF files: | This toolset can be used to perform the following operations on VCF files: | ||
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VCFtools consists of two parts, a perl module and a binary executable. The perl module is a general Perl API for manipulating VCF files, whereas the binary executable provides general analysis routines. | VCFtools consists of two parts, a perl module and a binary executable. The perl module is a general Perl API for manipulating VCF files, whereas the binary executable provides general analysis routines. | ||
== Installed version == | == Installed version == | ||
The currently installed | The currently installed versions of VCFTools are ... | ||
* '''VCFtools/0.1.14''' on ''hpc-uniol-env'' | |||
* '''VCFtools/0.1.15'''-intel-2017a-Perl-5.26.0 on ''hpc-uniol-new-env'' | |||
* '''VCFtools/0.1.16'''-GCC-8.3.0 on ''hpc-env/8.3'' | |||
== Using VCFtools == | == Using VCFtools == | ||
If you want to find out more about VCFtools on the HPC cluster, you can use the command | |||
module spider vcftools | |||
This will show you basic informations e.g. a short description and the currently installed version. | |||
To load the module, use the command | |||
module load VCFtools | |||
To load a specific version of VCFtools, you might need to change the environment and call for the specific version with <tt>module load</tt> | |||
module load hpc-env/8.3 | |||
module load VCFTools/0.1.16 | |||
Always remember: this command is case sensitive! | |||
<!--== Using VCFtools with the HPC cluster ==--> | |||
== Documentation == | == Documentation == | ||
The official documentation of VCFTools can be found [https://vcftools.github.io/examples.html here]. | |||
Latest revision as of 09:50, 22 July 2022
Introduction
VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.
This toolset can be used to perform the following operations on VCF files:
- Filter out specific variants
- Compare files
- Summarize variants
- Convert to different file types
- Validate and merge files
- Create intersections and subsets of variants
VCFtools consists of two parts, a perl module and a binary executable. The perl module is a general Perl API for manipulating VCF files, whereas the binary executable provides general analysis routines.
Installed version
The currently installed versions of VCFTools are ...
- VCFtools/0.1.14 on hpc-uniol-env
- VCFtools/0.1.15-intel-2017a-Perl-5.26.0 on hpc-uniol-new-env
- VCFtools/0.1.16-GCC-8.3.0 on hpc-env/8.3
Using VCFtools
If you want to find out more about VCFtools on the HPC cluster, you can use the command
module spider vcftools
This will show you basic informations e.g. a short description and the currently installed version.
To load the module, use the command
module load VCFtools
To load a specific version of VCFtools, you might need to change the environment and call for the specific version with module load
module load hpc-env/8.3 module load VCFTools/0.1.16
Always remember: this command is case sensitive!
Documentation
The official documentation of VCFTools can be found here.
