Table 1.

Tools included in the nf-core Sarek framework. The table reports the tool name, the sample type (G: germline, S: somatic), the variant type (SNV: small nucleotide variant, indel: small insertion/deletion, SV: structural variant, CNV: copy number variant, MSI: microsatellite instability), a small description of the core method, and the latest literature reference link.

Tool	Sample Type	Variant Type	Method	Ref
Manta	G, S	SV, indels	Graph-based breakend analysis	[57]
TIDDIT	G, S	SV	Coverage-based genome scan	[58]
Cnvkit	G, S	CNV	Coverage-based genome scan	[59]
Freebayes	G, S	SNV, indels	Haplotype-based Bayes theorem	[60]
Strelka2	G, S	SNV, indels	Haplotype-based mixture modeling	[61]
DeepVariant	G	SNV, indels	Pileup image CNN classification	[62]
HaplotypeCaller	G	SNV, indels	Haplotype re-assembly, likelihood	[63]
Mpileup	G	SNV, indels	Local re-alignment, likelihood	[55]
Mutect2	S	SNV, indels	GATK + read-to-haplotype alignment	[64]
Ascat	S	CNV	Signal intensity and allele frequency	[65]
Control-FREEC	S	CNV	LASSO-based genome segmentation	[66]
MSIsensor-pro	S	MSI	Multinomial distribution	[67]

Note. G: germline, S: Somatic; SV: Structural variant; SNV: small nucleotide variant, indel: small insertion/deletion; CNV: copy number variant, MSI: microsatellite instability.