Table 2.
Used tools and their versions in NGS somatic pipelines
| Tool and algorithm | Version |
|---|---|
| Trimmomatic | 0.3 |
| Reference Genome | GRCh38.d1.vd1 |
| bwa | 0.7.15 |
| bowtie2 | 2.3.5.1 |
| SAMtools | 1.8 |
| Picard | 2.17.11 |
| Qualimap | 2.2.2a |
| GATK4 | 4.3.0.0 |
| Strelka2 | 2.9.10 |
| SomaticSniper | 1.0.5.0 |
| vcftools | 0.1.16 |
| bcftools | 1.9 |
| PyVCF | 0.6.8 |
| NeuSomatic | 0.2.1 |
| SomaticSeq | 2.7.2 |
Trimmomatic was used for trimming. bwa and bowtie2 were used in mapping. SAMtools were used for converting SAM to BAM, indexing, and sorting. Picard was used to add readgroups and mark duplicates. The GATK4 tools used were BaseRecalibrator, ApplyBQSR, Mutect2, and SelectVariants. NeuSomatic and SomaticSeq were used for machine learning