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Table 2 Summary of SV genotyping methods

From: Comprehensive evaluation of structural variant genotyping methods based on long-read sequencing data

Category cuteSV LRcaller Sniffles SVJedi VaPoR
Version 1.0.11 0.2 1.0.12a 1.1.0 NA
Aligner minimap2, NGMLR minimap2, NGMLR minimap2, NGMLR minimap2 minimap2, NGMLR
SV type INSs, DELs, DUPs, INVs, TRAs INSs, DELs, DUPs, INVs, TRAs INSs, DELs, DUPs, INVs, TRAs INSs, DELs, INVs, TRAs INSs, DELs, DUPs, INVs
Data type CLR, CCS, ONT CLR, CCS, ONT CLR, CCS, ONT CLR, ONT CLR, CCS, ONT
Input REF, BAM, VCF REF, BAM, VCF BAM, VCF REF, VCF, FASTA/FASTQ; PAF, VCF REF, BAM, VCF/BED
Output 1 genotype 5 genotypes 1 genotype 1 genotype 1 genotype
  1. REF: the human reference genome; BAM: alignment in BAM (binary alignment map) format; VCF: targeted SVs in VCF (variant call format); FASTA/FASTQ: sequencing data in FASTA or FASTQ format; PAF: alignment in PAF (pairwise mapping format); BED: targeted SVs in BED (browser extensible data) format. “NA” indicates the data are not available. LRcaller employs five different genotyping models: direct (AD), variant alignment (VA), joint (J), presence (PR), and reference aware variant alignment (VAr), resulting in five genotypes [32]. We used the genotypes of the default joint model when comparing it with other SV genotyping methods