genome-references

Variant Callers

Mutect2- Tumor/normal or tumor only variant calling with local realignment
Vardict- Tumor/normal mode or tumor only
Strelka- Tumor/normal variant calling
Neusomatic-Tumor/normal with standalone mode or ensemble calling mode
Octopus- Tumor/normal or tumor only

Contamination

Conpair

Subclonality

Clonevol- Visualization of results
Fastclone

RNA-Seq Variant Calling Pipelines

CTAT-RNA-seek
GATK Best Practices
Deepvariant Germline RNA-seq

scRNA-seq Variant calling

cellsnp-lite- Uses population databases
SCExecute
SComatic
scAllele
cbSniffer

Others

Tabular ML for VC
TOSCA- Tumor Only Somatic Calling