vcftools
Link to section 'Description' of 'vcftools' Description
VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.
Link to section 'Versions' of 'vcftools' Versions
- Anvil: 0.1.14
Link to section 'Commands' of 'vcftools' Commands
- fill-aa
- fill-an-ac
- fill-fs
- fill-ref-md5
- vcf-annotate
- vcf-compare
- vcf-concat
- vcf-consensus
- vcf-contrast
- vcf-convert
- vcf-fix-newlines
- vcf-fix-ploidy
- vcf-indel-stats
- vcf-isec
- vcf-merge
- vcf-phased-join
- vcf-query
- vcf-shuffle-cols
- vcf-sort
- vcf-stats
- vcf-subset
- vcftools
- vcf-to-tab
- vcf-tstv
- vcf-validator
Link to section 'Module' of 'vcftools' Module
You can load the modules by:
module load vcftools
Link to section 'Example job' of 'vcftools' Example job
To run VCFtools on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=vcftools
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module load vcftools
vcftools --vcf input_data.vcf --chr 1 \
--from-bp 1000000 --to-bp 2000000