Open kelly-sovacool opened 4 months ago
Also compare to KFDRC somatic workflow https://github.com/kids-first/kf-somatic-workflow
Adapted from https://github.com/kids-first/kf-somatic-workflow?tab=readme-ov-file#somatic-variant-workflow-callers
Caller | CNV | SNV | SV | ecDNA | indel | - | KFDRC | NCI GDC | LOGAN | XAVIER |
---|---|---|---|---|---|---|---|---|---|---|
AmpliconArchitect | x | x | ? | ? | ||||||
CNVkit | x | x | ? | ? | ||||||
Control-FREEC | x | x | ? | ? | ||||||
GATK CNV | x | x | ? | ? | ? | |||||
Lancet | x | x | ? | ? | ||||||
Manta | x | ? | x | ? | ? | |||||
Mutect2 | x | x | x | x | ? | ? | ||||
Strelka2 | x | x | ? | ? | ||||||
THeTa2 | x | ? | x | ? | ? | |||||
VarDict | x | x | ? | ? | ||||||
MuSE | x | x | ? | ? | ||||||
VarScan2 | x | x | x | x | ? | ? | ||||
Pindel | x | x | ? | ? | ||||||
BRASS | x | x | ? | ? | ||||||
CaVEMan | x | x | ? | ? | ||||||
AscatNGS | x | x | ? | ? |
GDC: https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/DNA_Seq_Variant_Calling_Pipeline/