Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs using evidence from split-read alignments, high-mismatch regions, and coverage analysis. Please note the current version of Sniffles requires output from BWA-MEM! If you experience problems or have suggestions please contact: fritz.sedlazeck@gmail.com

INSTALL for Linux:

Download Sniffles:

git clone https://github.com/fritzsedlazeck/Sniffles

cd Sniffles

mkdir build

cd build

cmake ..

make

cd ../bin/

USAGE:

Please use BWA-MEM to align the reads using the parameters: “–M –x pacbio” . Reads do not need to be error corrected.

Sniffles requires a sorted bam file.

./sniffles -m reads.bam -v calls.vcf

Options:

 ./sniffles  -m <string> [-s <int>] [--max_num_splits <int>] [-q <int>]
           [-l <int>] [-v <string>] [--bede <string>] [-c <int>] [-t
           <int>] [-d <int>] [-n <int>] [--use_MD_Cigar] [--]
           [--version] [-h]

Where:

-m , --mapped_reads (required) Bam File

-s , --min_support Minimum number of reads that support a SV. Default: 10

--max_num_splits Maximum number of splits per read to be still taken into account. Default: 4

-q , --minmapping_qual Minimum Mapping Quality. Default: 20

-l , --min_length Minimum length of SV to be reported. Default:0

-v , --vcf VCF output file name

--bede Simplified format of bedpe Format.

-c , --min_cigar_event Minimum Cigar Event (e.g. Insertion, deletion) to take into account. Default:50

-t , --threads Number of threads to use. Default: 3

-d , --max_distance Maximum distance to group SV together. Default: 1kb

-n , --num_reads_report Report up to N reads that support the SV. Default: 0

--use_MD_Cigar Enables Sniffles to use the alignment information to screen for suspicious regions.

--, --ignore_rest Ignores the rest of the labeled arguments following this flag.

--version Displays version information and exits.

-h, --help Displays usage information and exits.

Sniffles version 0.0.1