Variant Calling Pipeline
BaseSpace Variant Interpreter accepts sample VCF files generated by the following variant callers regardless of aligner:
|
Variant Caller |
Analysis |
Variant Type |
|---|---|---|
|
DRAGEN* |
Somatic |
Indel, SNV, SV, and CNV |
|
Pisces (Somatic Variant Caller) |
Tumor only |
Indel, SNV, and MNV |
|
Strelka |
Germline, Tumor Normal |
Indel, SNV, and MNV |
* To ensure all variant types are loaded into the case, the small variant VCF must be present in the DRAGEN output files. Illumina recommends using the hard-filtered DRAGEN VCF output.