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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.

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Code (.tar.gz)

Installation

You can install Sniffles2 using pip or conda using:

 pip install sniffles 

or

 conda install sniffles=2.3.3

If you previously installed Sniffles1 using conda and want to upgrade to Sniffles2, you can use:

conda update sniffles=2.3.3

Quick start

To call SVs from long read alignments (PacBio / ONT), you can use:

 sniffles -i mapped_input.bam -v output.vcf.gz

This produces an output.vcf file, which includes all SVs that were called by the default parameter. Note you have to adjust the parameters for low coverage cases.

If you are interested in calling SVs across multiple samples:

First call each sample individually, including the snf tag

 sniffles --input sample1.bam --snf sample1.snf 

Combined calling using multiple .snf files into a single .vcf:

sniffles --input sample1.snf sample2.snf ... sampleN.snf --vcf multisample.vcf.gz

To call mosaic SVs, the --mosaic option should be added, i.e.:

sniffles --input mapped_input.bam --vcf output.vcf --mosaic