Next generation sequencing variant call criteria
| Nucleotide variation | Variant call criteria |
|---|---|
| SNV/INDEL | VAF: ≥5% in SNV |
| 5% in INDEL | |
| CNV | Amplification: avg. CNV ≥4 (gain), <1 (loss) |
| Translocation (fusion gene) | Read counts: ≥20 |
| Total valid mapped reads: ≥50,000 |
Variant detection/Interpretation: Ion Reporter V5.6, Oncomine Reporter.
Abbreviations: SNV/INDEL, single nucleotide variation/small insertions, deletion; VAF, variation allele frequency; CNV, copy number variation.
