snpgenie
Link to section 'Introduction' of '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.
Link to section 'Versions' of 'snpgenie' Versions
- 1.0
Link to section 'Commands' of 'snpgenie' 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
Link to section 'Module' of 'snpgenie' Module
You can load the modules by:
module load biocontainers
module load snpgenie
Link to section 'Example job' of 'snpgenie' Example job
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