Bcftools

Introduction

Bcftools is a program for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF.

Versions

• 1.13

• 1.14

• 1.17

• 1.20

Commands

• bcftools

• color-chrs.pl

• guess-ploidy.py

• plot-roh.py

• plot-vcfstats

• run-roh.pl

• vcfutils.pl

Example job

Adjust slurm options based on job requirements (slurm cheat sheet):

#!/bin/bash
#SBATCH -p partitionName  # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00  # Runtime limit (D-HH:MM:SS)
#SBATCH -N 1   # Number of nodes
#SBATCH -n 1   # Number of tasks per node
#SBATCH -c 4   # Number of CPU cores per task
#SBATCH --mem=8G       # Memory required per node
#SBATCH --job-name=bcftools    # Job name
#SBATCH --mail-type=FAIL,BEGIN,END     # Send an email when job fails, begins, and finishes
#SBATCH --mail-user=your.email@tufts.edu       # Email address for notifications
#SBATCH --error=%x-%J-%u.err   # Standard error file: <job_name>-<job_id>-<username>.err
#SBATCH --output=%x-%J-%u.out  # Standard output file: <job_name>-<job_id>-<username>.out

module purge   ### Optional, but highly recommended.
module load bcftools/XXXX      ### Latest version is recommended.