Table 5.
RTT NGS bioinformatic pipelines.
| RTT Laboratory | Data Analysis Tools/Pipelines | VAF | Minimum Coverage | Intron Flanking Region | Variant Annotation Databases |
|---|---|---|---|---|---|
| Lab1 | Ion ReporterTM Software Version 5.10 | 5% | 500× | ±10 bp | ClinVar, Varsome; COSMIC |
| Lab2 | MASTR Reporter 1.3.0 | 5% | 1000× | No | ClinVar; BRCA Exchange |
| Lab3 | novocraft V3.07.01, bamtools-2.4.1, VCFtools (0.1.15), bedtools v2.26.0-40, samtools 1.8, picardtools 2.8.3, ensembl vep release 94, CONTRA.v2.0.8, gatk-3.4.46 | 10% | 20× | NCBI, ClinVar, Ensembl, BRCA Exchange, cBioPortal | |
| Lab4 | Sophia DDM v3-Sophia Genetics | 5% | 500× | ClinVar, COSMIC, dbSNP, EXAC, g1000, ESP, EpiCov, GnomAD, | |
| Lab5 | Ion Reporter Software Version 5.16 | 5% | 100× | ±100 | dbSNP, BIC database, BRCA Exchange, BRCA Mutation Database |
RTT: Ring Test Trial; VAF: variant allelic frequency.