Cyvcf2

Introduction

Cyvcf2 is a cython wrapper around htslib built for fast parsing of Variant Call Format (VCF) files.

For more information, please check its website: https://biocontainers.pro/tools/cyvcf2 and its home page on Github.

Versions

0.30.14

Commands

cyvcf2
python
python3

Module

You can load the modules by:

module load biocontainers
module load cyvcf2

Interactive job

To run Cyvcf2 interactively on our clusters:

(base) UserID@bell-fe00:~ $ sinteractive -N1 -n1 -t1:00:00 -A myallocation
salloc: Granted job allocation 12345869
salloc: Waiting for resource configuration
salloc: Nodes bell-a008 are ready for job
(base) UserID@bell-a008:~ $ module load biocontainers scanpy/1.8.2
(base) UserID@bell-a008:~ $ python
Python 3.7.12 |  packaged by conda-forge |  (default, Oct 26 2021, 06:08:53)
[GCC 9.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from cyvcf2 import VCF

Batch job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Cyvcf2 on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=cyvcf2
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers cyvcf2

cyvcf2 --help
cyvcf2 [OPTIONS] <vcf_file>