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RUFUS k-mer based genomic variant detection
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runRufus.sh

README.md

RUFUS

K-mer based variant detection.

Andrew Farrell PhD
Director of Research and Science
Department of Human Genetics
USTAR Center for Genetic Discovery
Eccles Institute of Human Genetics
University of Utah School of Medicine​ 15 North 2030 East, Room 7140
Salt Lake City, UT 84112-5330
Email: JAndrewRFarrell@gmail.com
http://marthlab.org/

If you get errors during the installation contact me at at JAndrewRFarrell@gmail.com or submit an issue.

This project is still under development and not fully stable but free to use and any feedback is welcome.

Note: RUFUS is only supported on linux environments.

Installing RUFUS

1) Download

git clone https://github.com/jandrewrfarrell/RUFUS.git
cd RUFUS

2) Build

cd bin
cmake ../ -DCMAKE_C_COMPILER=/path/to/gcc-4.9.2 -DCMAKE_CXX_COMPILER=/path/to/g++-4.9.2
make

If you have gcc-4.9.2 as your default compiler, you may instead use

cd bin
cmake ../ -DCMAKE_C_COMPILER=$(which gcc) -DCMAKE_CXX_COMPILER=$(which g++)
make

RUFUS Requirements

RUFUS requires the use of the gcc-4.9.2 compiler. Please make sure that are using the gcc-4.9.2 compiler before you proceeed. If you are not using gcc-4.9.2 as your default compiler, or if CMake cannot detect the location of your gcc compiler, RUFUS will not build and install properly.

RUFUS requires Samtools. Please make sure that samtools is globally installed in your environment. RUFUS will not run without a working samtools.

Testing RUFUS

To make sure that RUFUS was successfully built, we provide users with a test run script to run RUFUS on a small test set of data with a small test reference, and default parameters. To test RUFUS, simply run

cd testRun
bash runTest.sh

NOTE: Make sure that runTest.sh is called directly from the testRun directory, or the testRun script will not be able to find the appropriate resources.

All data for this run is contained in the resources dir, and nothing needs to be provided by the user to test RUFUS.

At the end of a successfull test run, you should see a file named

testRun/Child.bam.generator.V2.overlap.hashcount.fastq.bam.vcf

This file should contain a single varient call. The call should look exactly as follows:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  ./Child.bam     Mother.bam      Father.bam
5:177630000     12896   X-DeNovo        T       G       25      PASS    RN=NODE_Child.bam.generator.V2_0_L273_D22:10:12::MH0;MQ=60;cigar=273M;SB=0.454545;CVT=X;HD=-1_-1_-1_-1_-1_19_-1_19_19_-1_-1_-1_-1_-1_20_20_19_-1_-1_18_-1_18_-1_-1_18_-1_-1_;AO=19;VT=X GT:DP:RO:AO     0/1:39:20:19    0/0:23:23:0     0/0:23:23:0

If you were unable to reproduce this call, something went wront with the RUFUS install, and you should get the test run to work before proceeding further. If you are unable to reproduce a successfull test run, please contact me at JAndrewRFarrell@gmail.com

Running

RUFUS is primarily used to find mutations unique to a proband sample, that are not found in the control samples

Usage:

./runRufus.sh [-s|--subject <arg>] [-c|--controls][<controls-1>] ... [<controls-n>]  [-t|--threads <arg>] [-k|--kmersize <arg>] [-r|--ref <arg>] [-m|--min <arg>] 
  [-h|--help]
-s,--subject: bam file containing the subject of interest (REQUIRED)

-c, --controls: bam files containing the control subjects (REQUIRED)

-t,--threads: number of threads to use (REQUIRED) (min 3)

-k,--kmersize: size of Kmer to use (REQUIRED)

-r,--ref: file path to the desired reference file to create VCF (REQUIRED)

-m,--min: overwrites the minimum k-mer count to call variant (OPTIONAL, Do not provide a min unless you are sure what you want)

-h,--help: HELP!!!!!!!!!!!!!!!

The command line should look something like this:

bash runRufus.sh --subject Child.bam --controls Mother.bam  --controls Father.bam  --kmersize 25 --threads 40 --ref human_reference_v37_decoys.fa

or

bash runRufus.sh -s Child.bam -c Mother.bam -c Father.bam -k 25 -t 40 -r human_reference_v37_decoys.fa

The flags can be provided any any order.

RUFUS can take any number control files (Must provide atleast one).

Each control Bam file requires a [-c|--controls] flag infront of the control file

For Example:

bash runRufus.sh -s tumorT1.bam -c tumorT0.bam -k 25 -t 40 -r human_reference_v37_decoys.fa

or

bash runRufus.sh -s Proband.bam -c Mother.bam -c Father.bam -c Sibling1.bam -c Sibling2.bam -k 25 -t 40 -r human_reference_v37_decoys.fa

We recommend a kmer size of 25, 40 threads, and to NOT provide RUFUS with the optional --min parameter

Providing a reference file.

After RUFUS has identified reads containing mutant kmers, the reads must be aligned to a reference fasta file. Any fasta file can be used as a reference, as long as the fasta file has been indexed for BWA. If a fasta has been indexed by bwa, there will be reference files with the following extensions: pac, .ann, .abm, .bwt, sa. In order to prepare a reference fasta for bwa, simply type:

bwa index -a bwtsw reference.fa
samtools faidx reference.fa

This will produce the BWA index files, and the fasta file index respectively. Make sure that the bwa index files and the fasta index file are in the same directory as reference.fa

Ubuntu dependencies

In order for RUFUS to run on a fresh Ubuntu build, all of the following packages must be installed:

General

sudo apt-get update
sudo apt-get install python
sudo apt-get install cmake
sudo apt-get install wget

GCC-4.9 (c/c++ compiler)

sudo apt-get install build-essential
sudo add-apt-repository ppa:ubuntu-toolchain-r/test
sudo apt-get install g++-4.9

zlib (file compression library)

sudo apt-get install zlib1g-dev
sudo apt-get install libbz2-dev

bzlib (bz2 file compression library)

sudo apt-get install libbz2-dev
sudo apt-get install liblzma-dev

bc (floating point precision library)

sudo apt-get install bc

Curse (terminal control library)

sudo apt-get install libncurses5-dev
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