CLCA_WGS

This repository contains software and analysis code used for the publication: Deep Whole Genome Analysis of 494 Hepatocellular Carcinomas.

Contents

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

Contact

If you have any questions or suggestions please contact us: Chong Zhang: zhang_c@pku.edu.cn