# :icon-sliders: Find structural variants
The [!badge corners="pill" text="snp"](../snp.md) module identifies single nucleotide
polymorphisms (SNP) and small indels, but you may want to (and should!) leverage the linked-read
data to identify larger structural variants (SV) like large deletions, duplications, and
inversions. Harpy provides two linked-read variant callers to do exactly that:

{.compact}
| Caller                    | variants it detects                        | caveats                           | link                                                                                                                                                               |
|:--------------------------|:-------------------------------------------|:----------------------------------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| [LEVIATHAN](leviathan.md) | inversion, duplication, deletion, breakend | requires supplementary alignments | [repo](https://github.com/morispi/LEVIATHAN), [paper](https://doi.org/10.1101/2021.03.25.437002)                                                                   |
| [NAIBR](naibr.md)         | inversion, duplication, deletion           | requires phased alignments        | [original repo](https://github.com/raphael-group/NAIBR), [fork repo](https://github.com/pontushojer/NAIBR), [paper](https://doi.org/10.1093/bioinformatics/btx712) |

## LEVIATHAN
LEVIATHAN relies on split-read information in the sequence alignments to call variants. It requires less
preprocessing work to get it up and running, so it's a great place to start.

## NAIBR
While our testing shows that NAIBR tends to find known inversions that LEVIATHAN misses, the program requires haplotype 
**phased** bam files as input. That means the alignments have a `PS` or `HP` tag that indicate
which haplotype the read/alignment belongs to. If your alignments don't have phasing tags (none of the current aligners in Harpy do this),
then you will need to use [!badge corners="pill" text="phase snp"](../Phase/phase_snp.md) and [!badge corners="pill" text="phase bam"](../Phase/phase_alignment.md).