whatshap
Link to section 'Introduction' of 'whatshap' Introduction
Whatshap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but works also well with short reads.
BioContainers: https://biocontainers.pro/tools/whatshap
Home page: https://github.com/whatshap/whatshap
Link to section 'Versions' of 'whatshap' Versions
- 1.4
Link to section 'Commands' of 'whatshap' Commands
- whatshap
Link to section 'Module' of 'whatshap' Module
You can load the modules by:
module load biocontainers
module load whatshap
Link to section 'Example job' of 'whatshap' 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 whatshap on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=whatshap
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers whatshap
whatshap phase --indels \
--reference=reference.fasta \
variants.vcf pacbio.bam