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. 2019 Apr 4;10(4):275. doi: 10.3390/genes10040275

Table 2.

Examples of bioinformatics tools that facilitate comprehensive genome analyses.

Authors Year Tool Method Input 1 Variants Detected Reference
Abyzov et al. 2011 CNVnator Read Depth PE2 Short read WGS Copy Number Variants [88]
Rausch et al. 2012 DELLY Paired-ends, Read depth, Split-reads Short read WGS Structural Variants [89]
Calabrese et al. 2014 MToolBox Read re-alignment WGS or WES Mitochondrial Variants [90]
Layer et al. 2014 LUMPY Paired-ends, Read depth, Split-reads PE short read WGS Structural Variants [91]
Roller et al. 2016 Canvas Read Depth WGS or WES Copy Number Variations [84,85]
Chen et al. 2016 Manta Pair Read, Split Read PE short read WGS Indels, Structural Variants [92]
Dolzhenko et al. 2017 Expansion-Hunter Sequence-graph PE short read WGS Large Expansion of Short Tandem Repeats [74]
Ebler et al. 2017 DIGTYPER Breakpoint-Spanning, Split Alignments PE short read WGS Inversions, Tandem Duplications [93]
Liang et al. 2017 Seeksv Split Read, Discordant Paired-End, Read Depth, 2 Ends Unmapped SE/PE 2 short read WGS Structural Variants + Virus Integration [94]
Mousavi et al. 2018 GangSTR Enclosing, Fully Repetitive, Spanning and Off-target Fully Repetitive Read Pairs PE short read WGS Tandem Repeat expansions [78]
Kim et al. 2018 Strelka2 Mixture-model PE short read WGS Single Nucleotide Variants, Indels [95]
Ye et al. 2018 Pindel Split-reads PE short read WGS Indels, Structural Variants (small and medium-size) [96,97]
Wala et al. 2018 SvABA Local assembly PE short read WGS Indels, Structural Variants (20–300 bp) [98]
Becker et al. 2018 SVE/FusorSV 8 SV callers combination + Data mining PE short read WGS Deletions + Duplications + Inversions 3 [86]
Antaki et al. 2018 SV2 Supervised support vector machine classifiers PE short read WGS Deletions + Duplications [87]

1 All tools take BAM files as input. MToolBoxaccepts FASTQ files. Strelka2, SV2, SvABA, ExpansionHunter, Manta also accept CRAM files, SV2 requires SVs to genotype, SNV VCF files and PED files. SVE/FusorSV accepts FASTQ, BAM and VCF files. SvABA also accepts SAM files. 2 PE = Paired-Ended; SE = Single-Ended 3 Other SVs could be explored if they are present in the training dataset.