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 with the optional SAM attributes enabled! If you experience problems or have suggestions please contact: fritz.sedlazeck@gmail.com
INSTALL:
Download Sniffles:
git clone https://github.com/fritzsedlazeck/Sniffles
cd Sniffles
mkdir build
cd build
cmake ..
make
cd ../bin/
USAGE:
./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 bede 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
--, --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 1.0.0