bcftools
Link to section 'Introduction' of 'bcftools' Introduction
Bcftools is a program for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF.
For more information, please check its website: https://biocontainers.pro/tools/bcftools and its home page on Github.
Link to section 'Versions' of 'bcftools' Versions
- 1.13
- 1.14
Link to section 'Commands' of 'bcftools' Commands
- bcftools
- color-chrs.pl
- guess-ploidy.py
- plot-roh.py
- plot-vcfstats
- run-roh.pl
- vcfutils.pl
Link to section 'Module' of 'bcftools' Module
You can load the modules by:
module load biocontainers
module load bcftools
Link to section 'Example job' of 'bcftools' 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 Bcftools on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=bcftools
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers bcftools
bcftools query -f '%CHROM %POS %REF %ALT\n' file.bcf
bcftools polysomy -v -o outdir/ file.vcf
# Variant calling
bcftools mpileup -f reference.fa alignments.bam | bcftools call -mv -Ob -o calls.bcf