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#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