Snpgenie

Introduction

Snpgenie is a collection of Perl scripts for estimating πN/πS, dN/dS, and gene diversity from next-generation sequencing (NGS) single-nucleotide polymorphism (SNP) variant data.

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

Versions

  • 1.0

Commands

  • fasta2revcom.pl

  • gtf2revcom.pl

  • snpgenie.pl

  • snpgenie_between_group.pl

  • snpgenie_between_group_processor.pl

  • snpgenie_within_group.pl

  • snpgenie_within_group_processor.pl

  • vcf2revcom.pl

Module

You can load the modules by:

module load biocontainers
module load snpgenie

Example 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 Snpgenie on our clusters:

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

module --force purge
ml biocontainers snpgenie

snpgenie.pl --minfreq=0.01 --snpreport=CLC_SNP_EXAMPLE.txt \
    --fastafile=REFERENCE_EXAMPLE.fasta --gtffile=CDS_EXAMPLE.gtf