Table 1 Structural variant (SV) callers in use at clinical sites.

	BaylorSeq	BCM	Duke/Columbia	Harvard	Miami	NIH	PacificNW	Stanford	UCLA	Utah	Vanderbilt	WUSTL
Find SVs from sequencing reads
Manta^a	■	■	□	□	□	□	□	□	■	■	□	■
ExpansionHunter		■			■				■	■		■
GATK^b		■		□		□			■
LUMPY					□	■				□		□
CNVnator					□				■			■
RUFUS		■								■
CNVkit								■				■
BreakDancer					□	■
Illumina DRAGEN depth-based CNV caller	■
SvABA: SV/indel Analysis by Assembly				■
CoNIFER^c							■
ERDS: estimation by reads depth w/ SNVs									■
BreakSeq2					□
DELLY2					□
Jointly call and/or genotype SVs
smoove							■			■		■
SVTyper					□					□		□
Annotate SVs
AnnotSV		■					■	■		■	■	■
gnomAD-SV					■							■
duphold										□		□
Run or combine output from other tools
XHMM		■		■		■
SURVIVOR					□							■
Parliament2					■

■ Tool called directly. □ Tool called indirectly (e.g., by a wrapper).
Each SV calling tool identifies subsets of SVs by type or other factors, and so in practice, the output of multiple methods must typically be combined and considered together. Wrapper tools that automatically call and combine results from multiple other SV detection methods improve the efficiency of this process. Duke/Columbia, NIH, Stanford, and Vanderbilt only use SV calling tools in specific cases or contexts rather than as part of their regular pipelines. Tool citations are listed in Extended Data Table 1.
CNV copy-number variant, SNV single-nucleotide variant.
^aManta is used by BaylorSeq to generate putative SV calls, which are then shared with the clinical sites.
^bThe two functions from GATK used are GermlineCNVCaller and DepthOfCoverage (DoC); the latter is used to detect exonic deletions or duplications.
^cIn contrast to other tools, CoNIFER runs on exome sequencing (ES) data rather than genome sequencing (GS) data.

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