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LoFreq

LoFreq is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data.

LoFreq is available as a module on Apocrita.

Usage

To run the default installed version of LoFreq, simply load the lofreq module:

$ module load lofreq
$ lofreq
Usage: lofreq <command> [options]

For full usage documentation, run lofreq without commands or options.

Example jobs

Serial jobs

Here is an example job running on 1 core and 2GB of memory, demonstrating the call subcommand:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=2G

module load lofreq

lofreq call -f ref.fa -o out.vcf in.bam

Here is an example job running on 4 cores and 8GB of memory, demonstrating the call-parallel subcommand:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 4
#$ -l h_rt=1:0:0
#$ -l h_vmem=2G

module load lofreq

lofreq call-parallel --pp-threads ${NSLOTS} -f ref.fa -o out.vcf in.bam

Here is an example job running on 4 cores and 8GB of memory, demonstrating the somatic subcommand:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 4
#$ -l h_rt=1:0:0
#$ -l h_vmem=2G

module load lofreq

lofreq somatic -n normal-sample.bam -t tumor-sample.bam -f ref.fa \
    --threads ${NSLOTS} -o out_file_prefix

References