Mapcaller

Introduction

Mapcaller is an efficient and versatile approach for short-read mapping and variant identification using high-throughput sequenced data.

For more information, please check its website: https://biocontainers.pro/tools/mapcaller and its home page on Github.

Versions

• 0.9.9.41

Commands

• MapCaller

Module

You can load the modules by:

module load biocontainers
module load mapcaller

Example job

Warning

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 Mapcaller on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 12
#SBATCH --job-name=mapcaller
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers mapcaller

MapCaller index ref.fasta ref

MapCaller -t 12 -i ref -f input_1.fastq  -f2 input_2.fastq  -vcf out.vcf