This repository contains software and analysis code used for the publication: Deep Whole Genome Analysis of 494 Hepatocellular Carcinomas.
| Category | Function | Software | Version | Container name |
|---|---|---|---|---|
| 1 | Mutation calling | BWA | 0.7.12 | mutation_calling.sif |
| 1 | Mutation calling | FASTP | 0.13.1 | mutation_calling.sif |
| 1 | Mutation calling | Mutect2 | 4.0.11.0 | mutation_calling.sif |
| 1 | Mutation calling | sambamba | 0.6.8 | mutation_calling.sif |
| 1 | Mutation calling | samtools | 1.4 | mutation_calling.sif |
| 1 | Mutation calling | Strelka | 2.8.4 | strelka.sif |
| 2 | Identification of candidate drivers | ActiveDriverWGS | 1.1.1 | driver.sif |
| 2 | Identification of candidate drivers | dndscv | 0.1.0 | driver.sif |
| 2 | Identification of candidate drivers | MutSig2CV_NC | Only one version | driver.sif |
| 2 | Identification of candidate drivers | NBR | Only one version | driver.sif |
| 2 | Identification of candidate drivers | pvalue_combination | Only one version | driver.sif |
| 2 | Identification of candidate drivers | OncodriveFML | 2.3.0 | oncodrivefml.sif |
| 3 | Mutational signature extraction and assignment | mSigHdp | 1.1.2 | signature.sif |
| 3 | Mutational signature extraction and assignment | SigProfilerExtractor | 1.1.0 | signature.sif |
| 3 | Mutational signature extraction and assignment | mSigAct | 2.2.3 | signature.sif |
| 4 | SV and clustered mutational events | maftools | 2.6.05 | SV_CNA_ecDNA.sif |
| 4 | SV and clustered mutational events | Shatterseek | 0.4 | SV_CNA_ecDNA.sif |
| 4 | SV and clustered mutational events | lumpy | 0.2.13 | SV_CNA_ecDNA.sif |
| 5 | CNA calling | purple | 2.34 | SV_CNA_ecDNA.sif |
| 5 | CNA calling | Sequenza | 2.1.1 | SV_CNA_ecDNA.sif |
| 6 | Detection of ecDNA | AmpliconClassifier | 0.2.5 | SV_CNA_ecDNA.sif |
| 7 | Inferring clonality and evolutionary history | MutationTimeR | 0.99.3 | clonality_RNA.sif |
| 7 | Inferring clonality and evolutionary history | PhylogicNDT | Only one version | clonality_RNA.sif |
| 7 | Inferring clonality and evolutionary history | PyClone | 0.13.1 | clonality_RNA.sif |
| 7 | Inferring clonality and evolutionary history | Timing_and_Signatures | Only one version | clonality_RNA.sif |
| 8 | RNA data analysis | RSEM | 1.3.3 | clonality_RNA.sif |
| 8 | RNA data analysis | STAR | 2.7.3a | clonality_RNA.sif |
If you have any questions or suggestions please contact us: Chong Zhang: zhang_c@pku.edu.cn
