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