# Find structural variants

The snp 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:

aligner	recommended	variants it detects	caveats	link
NAIBR	✅	inversion, duplication, deletion	requires phased alignments	original repo, fork repo, paper
LEVIATHAN		inversion, duplication, deletion, breakend	requires supplementary alignments	repo, paper

# Caveats

# 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 the phase module to phase your SNPs into haplotypes so the sv naibr module can use that to phase your input alignments and proceed as planned.

# LEVIATHAN

LEVIATHAN relies on split-read information in the sequence alignments to call variants. The EMA aligner does not report split read alignments, instead it reports secondary alignments. It is recommended to use BWA- or strobealign-generated alignments if intending to call variants with sv leviathan .