ganqiao1990 / clca_wgs

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: [email protected]