Parameter

Command line Interface

   ./sniffles  -m <string> [-s <int>] [-f <float>] [-v <string>] [-b
                                        <string>] [--max_num_splits <int>]
                                        [-q <int>] [-l <int>] [-t <int>]
                                        [-d <int>] [--tmp_file <string>]
                                        [-r <int>] [-z <int>] [-n <int>]
                                        [--cluster_support <int>] [--Ivcf
                                        <string>] [--report_seq]
                                        [--report_BND] [--ignore_sd]
                                        [--cluster] [--genotype] [--]
                                        [--version] [-h]

Parameter

Input

---

-m/--mapped_reads

Sorted .bam file either form NGM-LR or BWA-MEM (please use -M flag during mapping with BWA)

Output

Sniffles support vcf and bedpe output format, but you have to specify one:

-v/--vcf	Name of the vcf file to be reported
-b/--bedpe	Name of the bedpe file to be reported

General (most important first)

-s/--min_support	Minimum number of reads that support a SV to be reported. Default: 10
-d/--max_distance	Maximum distance to group SV together. Sniffles estimates this parameter during runtime to group together SVs reported by different reads. Default: 1kb
--max_num_splits	Maximum number of split segments a read is aligned at before it is ignored. Default: 7
-l/--min_length	Minimum length of SV to be reported. Default: 30bp
--genotype	Performs genotype estimation.
--cluster	Performs read based phasing to mark SVs that occur together.
-q/--minmapping_qual	Minimum mapping quality of alignment to be taken into account. Default: 20
-n/--num_reads_report	Number of read names to be reported that support the SV in the vcf file. Default: 0
-r/--min_seq_size	Discard read if non of its segment is larger then this. Default: 2kb
-z/--min_zmw	Discard SV that are not supported by at least x zmws. This applies only for PacBio recognizable reads. Default: 0
-t/--threads	Maximum number of threads to use. Note this is currently not supported. Default: 3
--Ivcf	Provided vcf file that enables forced calling. Default : ""
--tmp_file	Optional path to write tmp files to. Default : .
--ignore_sd	Ignores the sd based filtering. default: false
--report_BND	Reports the inversions and translocations as BND events. Default: false
--report_seq	Reports the sequences for insertions and deletions events. Default: false
-f/--allelefreq	Filters the SV calls based on the allele frequency. Default: 0.0
--version	Shows the current version.
-h/--help	Shows the help message.