#FERMI ##Fast Extremely Rare Mutation Identification
FERMI is used to identify mutations at an extremely rare frequency. The program is fully function at the moment, but missing a great deal of functionality that will be added in the future to increase useability.
####Usage Instructions Please see the FERMI Homepage for download and usage instructrions. This page will be progressively updated to be as complete as possible.
##Installation The following instructions are for Debian Linux, but with some adjustment should work anywhere.
Download FERMI
git clone https://github.com/liggettla/FERMI
Install bwa
sudo apt-get install bwa
Download freebayes
git clone --recursive git://github.com/ekg/freebayes.git
cd freebayes
make
##Example Runs Take input files from testInput and put analyzed files in testOutput:
./fermi.py -i testInput/ -o testOutput/
Submit run to computing cluster:
./fermi.py -c -i testInput/ -o testOutput/
Allow 2 UMI mismatches, 0.6 variant threshold and 3 supporting reads of a UMI pair:
./fermi.py -u 2 -v 0.6 -r 3 -i testInput/ -o testOutput/
Output all fastq files generated in the analysis:
./fermi.py -l -i testInput/ -o testOutput/
Avoid alignment and variant calling for testing:
./fermi.py -a -i testInput/ -o testOutput/
"Where is everybody?!"
####Help File optional arguments:
-h, --help show this help message and exit
--nfo NFO, -n NFO Info writeup about a particular run that will be output in the run directory.
--largefiles, -l Outputs all generated fastq files generated during analysis.
--avoidalign, -a Only runs through initial analysis of input fastq files, and does not align to reference or call variants.
--outdir OUTDIR, -o OUTDIR Specifies output directory where all analysis files will be written
--indir INDIR, -i INDIR Specifies the input directory that contains the fastq files to be analyzed.
--single, -s Only process a single set of paired end reads.
--prevdict PREVDICT, -p PREVDICT Specify a previously output pickle file containing collapsed fastq data as an input instead of raw fastq files.
--umimismatch UMIMISMATCH, -u UMIMISMATCH Specify the number of mismatches allowed in a UMI pair to still consider as the same UMI
--varthresh VARTHRESH, -v VARTHRESH Specify the percentage of reads that must contain a particular base for that base to be used in the final consensus read
--readsupport READSUPPORT, -r READSUPPORT Specifies the number of reads that must have a given UMI sequence in order to be binned as a true capture event, and not be thrown out.
--clustersubmit, -c Submit run to cluster computing rather than running locally