Resources
Reference genomes¶
The Initial QC and variant calling pipelines support the following genomes:
Human hg19 hg38
Mouse mm10
Tools and versions¶
| Analysis Category | Software | Version | Notes |
|---|---|---|---|
| Preprocessing | |||
| Trimmomatic | 0.33 | ||
| bwa aligner | 0.7.15 | ||
| Picard | 2.1.1 | ||
| Genome Analysis Toolkit (GATK) | 3.8-0 | ||
| Somatic Variant Calling | |||
| Mutect2 | GATK 3.8-0 | ||
| Mutect | 1.1.7 | ||
| VarDict | 1.4 | ||
| Strelka | 2.9.0 | Tumor-Normal only | |
| vcf2maf | 1.6.16 | ||
| MutSigCV | 1.41 | Run only if >10 tumor samples | |
| Germline Variant Calling | |||
| HaplotypeCaller | GATK 3.8-0 | ||
| Admixture | 1.3.0 | ||
| PLINK | 1.9.0 | ||
| Copy Number Variants (CNV) | |||
| Control-FREEC | 11.9 | Tumor-Normal only | |
| Sequenza-utils | 2.2.0 | Tumor-Normal only | |
| Sequenza R package | 3.0 | Tumor-Normal only | |
| Canvas | 1.3.8 | WGS only | |
| Structural Variants (SV) | |||
| Manta | 1.3.0 | ||
| SvABA | WGS only | ||
| Quality Control and Reporting | |||
| qualimap | 2.2.1 | ||
| multiqc | 1.4 | ||
| FastQC | 0.11.5 | ||
| Fastq Screen | 0.9.3 | ||
| General scripting | |||
| R | 3.5 | ||
| perl | 5.18.4 | ||
| Python | 3.6 |
Last update: 2022-11-04