Table 1 Features of the variant calling tools that were compared for somatic variant detection from IONT data
From: Comparison of somatic variant detection algorithms using Ion Torrent targeted deep sequencing data
Somatic variant caller | Statistical Method | Version | Variant Types | Somatic Variation Identification strategy | Input | Output |
|---|---|---|---|---|---|---|
Torrent Variant Caller (TVC) | Subtraction | 4.2 | Somatic, germline | Call tumour and normal sample separately | Original BAM file | VCF file |
MuTect2 | Bayesian classifier | 4.0 | Somatic | Call paired tumour-normal or tumour-only samples | Sorted, indexed BAM file | VCF file |
VarScan2 | Fisher’s Exact Test | 2.2.3 | Somatic, germline | Call paired tumour-normal sample only | Pileup BAM file | VCF file |