Table 1 A comparison of features between SomatoSim and existing somatic variant simulation tools
From: SomatoSim: precision simulation of somatic single nucleotide variants
SomatoSim | VarSim | SInC | DWGSIM | GemSim | tHapMix | Xome-Blender | BAMSurgeon | |
|---|---|---|---|---|---|---|---|---|
Variants introduced into experimentally generated reads | ✓ | X | X | X | X | ✓ | ✓ | ✓ |
User definable VAFs | ✓ | X | X | X | ✓ | X | X | ✓ |
User definable depth of coverage | ✓ | ✓ | ✓ | ✓ | X | ✓ | ✓ | ✓ |
MQ and BQ control | ✓ | X | X | X | X | X | X | X |
User definable separation distance between randomly simulated SNVs | ✓ | X | X | X | X | X | X | X |
Strand distribution modeling | ✓ | X | X | X | X | X | X | X |
Types of somatic variants | SNV | SNV, Indel, SV | SNV, Indel, CNV | SNV, Indel | SNV | SNV, CNV | SNV, Indel, CNV | SNV, Indel, CNV, SV |
Output data type | BAM | FASTQ | FASTQ | FASTQ | FASTQ | BAM | BAM | BAM |