# 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:

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

# 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 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.