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What is Sniffles?

Sniffles is a SV caller for long reads. It is mainly designed for PacBio reads, but also works on Oxford Nanopore reads. SV are larger events on the genome (e.g. deletions, duplications, insertions, inversions and translocations). Sniffles can detect all of these type and more such as nested SVs (e.g. inversion flanked by deletions or an inverted duplication). Furthermore, Sniffles incorporates multiple auto tuning functions to determine data set depending parameter to reduce the overall risk of falsely infer SVs.

Quick Start

Make sure you have a sorted bam file either from ngmlr or from bwa. For the later make sure you have used -M parameter for mapping to mark which alignments are primary and which are secondary! Note you have to adjust the parameters for low coverage cases.

Parameters

General

Parameter	Description
Minimum Support	Minimum number of reads that support a SV to be reported. Default: 10
Maximum Number of Splits	Maximum number of split segments a read is aligned at before it is ignored. Default: 7
Maximum Distance	Maximum distance to group SV together. Sniffles estimates this parameter during runtime to group together SVs reported by different reads. Default: 1kb
Minimum Length	Minimum length of SV to be reported. Default: 30bp
Minimum Mapping Quality	Minimum mapping quality of alignment to be taken into account. Default: 20
Number of Reads to Report	Number of read names to be reported that support the SV in the vcf file. Default: 0
Minimum Seq Size	Discard read if none of its segment is larger then this. Default: 2kb
Minimum ZMW	Discard SV that are not supported by at least x zmws. This applies only for PacBio recognizable reads. Default: 0
Enable CS String	Enables the scan of CS string instead of Cigar and MD. Default: False

Clustering Options

Parameter	Description
Cluster	Performs read based phasing to mark SVs that occur together.
Cluster Support	Minimum number of reads supporting clustering of SV. Default: 1
Allele Frequency Threshold	Filters the SV calls based on the allele frequency. Default: 0.0
Minimum Homogenous Allele Frequency	Minimum homogeneous threshold on allele frequency. Default: 0.8
Minimum Heterogeneous Allele Frequency	Minimum heterogeneous threshold on allele frequency. Default: 0.3

Advanced Options

Parameter	Description
Report BND	Reports the inversions and translocations as BND events. Default: False
Don't Report Seq	Don't report sequences for indels in vcf output. (Beta version!) Default: False
Ignore sd	Ignores the sd based filtering. Default: False
CCS Reads	Preset CCS Pacbio setting. (Beta) Default: False

Parameter Estimation Options

Parameter	Description
Skip Parameter Estimation	Enables the scan if only very few reads are present. Default: False
Estimated Deletion Ratio	Estimated ratio of deletions per read. Default: 0.0458369
Estimated Insertion Ratio	Estimated ratio of insertions per read. Default: 0.049379
Maximum Differences Per Window	Maximum differences per 100bp. Default: 50
Maximum Distance Between Alignment Events	Maximum distance between alignment (indel) events. Default: 4

Output

VCF Info field description | Sniffles report multiple information in the Info field. The entries are delimited by: | +-------------------+------------------------------------------------------------------------------------------------------+ | IMPRECISE/PRECISE | Indicates the confidence of the exact breakpoint positions (bp). | +-------------------+------------------------------------------------------------------------------------------------------+ | CHR2= | The chromosome of the second breakpoint of the SV reported. | +-------------------+------------------------------------------------------------------------------------------------------+ | END= | The position (bp) of the second breakpoint of the SV reported. | +-------------------+------------------------------------------------------------------------------------------------------+ | ZMW= | For PacBio based reads, shows the number of ZMW that support the SV. | +-------------------+------------------------------------------------------------------------------------------------------+ | SVTYPE= | The type of the SV. (see Alt field above) | +-------------------+------------------------------------------------------------------------------------------------------+ | SUPTYPE= | Indicates what evidence supports the SVs (SR: Split Reads, AL: Alignment, NR: Noisy Region). | +-------------------+------------------------------------------------------------------------------------------------------+ | STD_quant_start= | The standard deviation of the start breakpoints. | +-------------------+------------------------------------------------------------------------------------------------------+ | STD_quant_stop= | The standard deviation of the stop breakpoints. | +-------------------+------------------------------------------------------------------------------------------------------+ | RNAMES= | A comma separated list of read names that support the SV event. Controlled by -n Parameter. | +-------------------+------------------------------------------------------------------------------------------------------+ | SVLEN= | Indicates the length of SVs. | +-------------------+------------------------------------------------------------------------------------------------------+ | STRANDS= | Strand information at both breakpoints. | +-------------------+------------------------------------------------------------------------------------------------------+ | SEQ= | If reportable shows the sequence of the indels. | +-------------------+------------------------------------------------------------------------------------------------------+ | RE= | Number of reads supporting the variance. | +-------------------+------------------------------------------------------------------------------------------------------+ | AF= | Allele frequency (only if run with –genotype) | +-------------------+------------------------------------------------------------------------------------------------------+ | Source: https://github.com/fritzsedlazeck/Sniffles/wiki