vcf2phylip
Link to section 'Introduction' of 'vcf2phylip' Introduction
vcf2phylip is a tool to convert SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis.
Home page: https://github.com/edgardomortiz/vcf2phylip
Link to section 'Versions' of 'vcf2phylip' Versions
- 2.8
Link to section 'Commands' of 'vcf2phylip' Commands
- vcf2phylip.py
Link to section 'Module' of 'vcf2phylip' Module
You can load the modules by:
module load biocontainers
module load vcf2phylip
Link to section 'Example job' of 'vcf2phylip' 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 vcf2phylip on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=vcf2phylip
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers vcf2phylip
vcf2phylip --input myfile.vcf