{"id":8402,"date":"2024-10-31T15:09:58","date_gmt":"2024-10-31T15:09:58","guid":{"rendered":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/?page_id=8402"},"modified":"2024-10-31T15:09:58","modified_gmt":"2024-10-31T15:09:58","slug":"lofreq","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/lofreq\/","title":{"rendered":"LoFreq"},"content":{"rendered":"

Overview<\/h2>\n

LoFreq*<\/a>(i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. <\/p>\n

Version 2.1.5 is installed on the CSF. This has been compiled from source against HTSLib 1.20.<\/p>\n

Restrictions on use<\/h2>\n

There are no restrictions on accessing the software on the CSF.<\/p>\n

You must cite your usage of LoFreq – please see the citation page<\/a> for details.<\/p>\n

Set up procedure<\/h2>\n

We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for how to do this. Alternatively, you may load modulefiles on the login node and let the job inherit these settings<\/abbr>.<\/p>\n

Load one of the following modulefiles:<\/p>\n

\r\nmodule load apps\/gcc\/lofreq\/2.1.5\r\n<\/pre>\n
Running the application<\/h2>\n
Please do not run LoFreq on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n
You may view the help text by running the following on the login node, after loading the modulefile:<\/p>\n
\r\nlofreq                 # Will show the list of commands supported\r\nlofreq call            # Help about the \"call\" command\r\nlofreq call-parallel   # Help about the \"call-parallel\" command\r\nlofreq command<\/em>         # Help about command<\/em>\r\n<\/pre>\n
Serial batch job submission<\/h3>\n
Create a batch submission script (which will load the modulefile in the jobscript), for example:<\/p>\n
\r\n#!\/bin\/bash --login\r\n#$ -cwd             # Job will run from the current directory\r\n                    # NO -V line - we load modulefiles in the jobscript\r\n\r\nmodule load apps\/gcc\/lofreq\/2.1.5\r\n\r\nlofreq call options<\/em> in<\/em>.bam\r\n\r\n# For example:\r\nlofreq call -f ref.fa -o vars.vcf aln.bam\r\n<\/pre>\n
Submit the jobscript using: <\/p>\n
qsub scriptname<\/em><\/pre>\n
where scriptname<\/em> is the name of your jobscript.<\/p>\n
Parallel batch job submission<\/h3>\n
Create a batch submission script (which will load the modulefile in the jobscript), for example:<\/p>\n
\r\n#!\/bin\/bash --login\r\n#$ -cwd\r\n#### Now choose one<\/strong> of the following parallel environments\r\n#$ -pe smp.pe  8      # Intel hardware, 2--32 cores. Use this for high-memory jobs too.\r\n## OR\r\n#$ -pe amd.pe  8      # AMD Genoa hardware, 2-168 cores.\r\n\r\n# The smp.pe environment can run high-memory jobs. Add extra flags as needed (check the docs.)\r\n\r\nmodule load apps\/gcc\/lofreq\/2.1.5\r\n\r\nlofreq call-parallel --pp-threads $NSLOTS options<\/em> in<\/em>.bam\r\n\r\n# For example\r\nlofreq call-parallel --pp-threads $NSLOTS -f ref.fa -o vars.vcf aln.bam\r\n                                    #\r\n                                    # Will be replaced by the number of cores requested above\r\n\r\n# The somatic command\r\nlofreq somatic --threads $NSLOTS -n normal.bam -t tumor.bam -f hg19.fa  -o out_ [-d dbsnp.vcf.gz]\r\n                  #\r\n                  # The somatic command uses --threads (not --pp-threads)\r\n<\/pre>\n
Submit the jobscript using: <\/p>\n
qsub scriptname<\/em><\/pre>\n
where scriptname<\/em> is the name of your jobscript.<\/p>\n
Further info<\/h2>\n