The following tools are used for calling of small variants and annotation of small variants:
| step | tool | version | comments |
|---|---|---|---|
| Variant calling - hla | HLA-genotyper | 2022_05 | https://github.com/axelgschwind/hla-genotyper |
| Variant calling - SNVs and Indels | Strelka2 | 2.9.10 | (tumor-normal) |
| Variant calling - SNVs and Indels | Varscan2 | 2.4.5 | (tumor-only) |
| Variant calling - left-normalization of InDels | VcfLeftNormalize | ngs-bits latest | |
| Annotation - b-allele frequency (t/n) | VariantAnnotateFrequency | ngs-bits latest | |
| Annotation - general | VEP | 109.3 |
CNV calling and annotation is performed using these tools:
| step | tool | version | comments |
|---|---|---|---|
| CNV calling | ClinCNV | 1.18.3 | |
| annotation - general | BedAnnotateFromBed | ngs-bits latest | Several data sources are annotated using this tool. (tumor-only) |
| annotation - gene information | CnvGeneAnnotation | ngs-bits latest | |
| annotation - overlapping pathogenic CNVs from NGSD | NGSDAnnotateCNV | ngs-bits latest |
SV calling and annotation is performed using these tools:
| step | tool | version | comments |
|---|---|---|---|
| SV calling | Manta | 1.6.0 | |
| annotation - gene information | BedpeGeneAnnotation | ngs-bits latest |
Viral load:
| step | tool | version | comments |
|---|---|---|---|
| Filtering reads | samtools | 1.17 | |
| Mapping | bwa mem2 | 2.2.1 | |
| Variant calling | freebayes | 1.3.6 | |
| Statistics - Coverage | BedCoverage | ngs-bits latest | |
| Statistics - BedReadCount | BedReadCount | ngs-bits latest | |
| Annotation | BedAnnotateFromBed | ngs-bits latest | Several data sources are annotated using this tool. |
Microsatellite instability (MSI):
| step | tool | version | comments |
|---|---|---|---|
| Calling | Mantis | 1.0.5 |