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Table 1 Software for predicting structural variations

From: Unraveling genomic variation from next generation sequencing data

Tool Single-End Pair-End Reference genome Insertion Deletion Inversion Translocation across chromosomes Translocation within chromosome Properties Input File
BreakDancer [61]   X   X X X X X • BreakDancerMax for large regions and BreakDancerMini for indels of 10-100 bp BAM, SAM
CNV-seq [62] X   X X X     Shotgun sequencing Map locations from a BAM file (by SAM tools)
Robust statistical model
GASV [63]   X   X X X X X Geometric approach BAM
A SV is pictured as a polygon on a surface
Comparison of SVs across multiple samples
HyDRa [64]   X   X X X X X SV breakpoints by clustering discordant paired-end alignments Tab-delimiteddiscordant paired-end mappings
MoDIL [65]   X   X X     Medium sized (10-50 bp) paired-end indels Software specific
Able identify shorter heterozygous, as well as homozygous variants with higher accuracy  
MrFast [66] X    X X     Short sequence reads (>25 bp) FASTA, FASTQ
NovelSeq [67]   X   X      Long novel sequence insertions Software specific
Multiple types of variations
PEMer [68]   X   X X X X X • PEMer: variations SVdB API
• SV-Simulation: simulated paired-end reads
• BreakDB: annotations
Pindel [69]   X X X X     Large deletions (1 bp–10 kb) BAM,SAM,FASTA, FASTQ
Medium sized insertions (1–20 bp) from 36 bp paired-end short reads
rSW-seq [70] X   X X X     Based on an iterative Smith-Waterman dynamic sequence alignment method Tab-delimited file denoting the tumor/normal status for each of aligned read positions
VariationHunter [71]   X   X X X    Evaluation of the entire possible mapping set of positions of each paired-end read and final mapping of the SVs interdependently. Software specific
VarScan [72, 73] X   X X X     Germline variants (SNPs and indels) in individual samples or pools of samples. Pileup, VCF
Shared and private variants in multi-sample datasets (with mpileup).
Somatic mutations, LOH events, and germline variants in tumor-normal pairs.
          Somatic copy number alterations (CNAs) in tumor-normal exome data.