Software: Snpgenie
Description
Snpgenie is a collection of Perl scripts for estimating ?N/?S, dN/dS, and gene diversity from next-generation sequencing (NGS) single-nucleotide polymorphism (SNP) variant data.
Available Versions
| Unspecified: | 1.0 |
|---|
For more information, please check its website: https://biocontainers.pro/tools/snpgenie and its home page on Github.
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
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
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