Table 4.

List of RNA-seq somatic and germline SNV callers sorted in alphabetical order. For each variant caller, the types of variants that are reported (column 2), whether DNA-RNA integrated analysis is performed (column 3), whether the tool is exclusively for RNA-seq variant calling (column 4), and whether a complete workflow including RNA-seq read mapping, variant calling, and filtering is provided (column 6) are presented. The variant callers and their core algorithms are explained in detail in Section 6.

Variant caller	Type of variant	Integrated analysis	Dedicated to RNA-seq	Complete workflow
eSNV-detect [81]	SNV	No	Yes	No
RADIA [26]	SNV	Yes	No	No
Seurat [33]	SNV, indel	Yes	No	No
SNPiR [80]	SNV	No	Yes	Yes
VarDict [18]	SNV, indel, SV	No	No	No
VarScan2 [9]	SNV, indel	No	No	No