Comparative assessments of indel annotations in healthy and cancer genomes with next-generation sequencing data

BMC Medical Genomics

Table 1 A list of indel calling programs

Programs	General /somatic	Type of variants	Core algorithms	Notes and references
Dindel	General	Indel	Alignment-based	Bayesian approach [13]
GATK_HC	General	SNP + Indel	Haplotype-based	Collection of candidate haplotypes [14]
GATK_UG	General	SNP + Indel	Alignment-based	Bayesian genotype likelihood model [15]
Pindel	General	Indel	Split read mapping	A pattern growth approach [16]
Platypus	General	SNP + Indel	Haplotype-based	Collection of candidate haplotypes [17]
SAMTools	General	SNP + Indel	Alignment-based	Bayesian model [18]
Varscan	General	SNP + Indel	Alignment-based	Heuristic method [19]
GATK Mutect2	Somatic	SNP + Indel	Allele frequency	Re-assembly of haplotypes methods [20, 21]
Strelka	Somatic	SNP + Indel	Allele frequency	Bayesian approach [22]
Strelka2	Somatic	SNP + Indel	Allele frequency	A mixture model [23]
Varscan2	Somatic	SNP + Indel	Heuristic methods	Heuristic and statistical methods [24]

ISSN: 1755-8794