Sniffles

Sniffles (SV caller)

• Author: Dreycey Albin
• Date: 05/10/2019
• Updates: NAME (DATE): update descr; NAME (DATE): update descr,
• Sniffles is used for finding structural variants
• documentation (website): Sniffles GitHub
• documentation (publication): Nature-Sniffles

Installation

INSTRUCTIONS ON HOW TO INSTALL USING TERMINAL

• installation for MacOS

wget https://github.com/fritzsedlazeck/Sniffles/archive/master.tar.gz -O Sniffles.tar.gz
tar xzvf Sniffles.tar.gz
cd Sniffles-master/
mkdir -p build/
cd build/
cmake -D CMAKE_C_COMPILER=/opt/local/bin/gcc-mp-4.7 -D CMAKE_CXX_COMPILER=/opt/local/bin/g++-mp-4.7 ..

cd ../bin/sniffles*
./sniffles

• installation for Linux

wget https://github.com/fritzsedlazeck/Sniffles/archive/master.tar.gz -O Sniffles.tar.gz
tar xzvf Sniffles.tar.gz
cd Sniffles-master/
mkdir -p build/
cd build/
cmake ..
make

cd ../bin/sniffles*
./sniffles

Basic commands

INPUT

• input is taken in as a bam file. This should be the output of all the mapping softwares.

./sniffles -m reads_region.bam -v test.vcf

OUTPUT

outputfile.vcf

Example_1

Input files

• Use the example given in the samples

ls test_set/

commands

`* Run the general Sniffles command:

./bin/sniffles-core-1.0.11/sniffles -m test_set/reads_region.bam -v outputname.vcf

Output files

• VCF as output

outputname.vcf