Tools Description

Versions of tools in order of process

Tool	Version
VarDict	1.8.2
Post Processing Variant - Single Sample FIlter	0.1.5
BCFtools - sort, normalize, bgzip, tabix	1.15.1
BCFtools - concat	1.6
SnpSift - annotate	5.0
vcf2maf	1.6.21
OncoKB - annotator	3.2.2
Post Processing Variant - MAF annotated by BED	0.2.3
Post Processing Variant - MAF annotated by TSV	0.2.3
Post Processing Variant - MAF tag	0.2.3
Post Processing Variant - MAF filter	0.2.3

Files and Resources used

There are multiple files from different resources used in this workflow.

Steps	Database,Version	File
SnpSIFT annotate	Cosmic V96	1. overall prevalence is obtained from CosmicCodingMuts.normal.vcf.gz (Note: normal denotes normalized ) 2. lineage prevalence was obtained by processing CosmicCodingMuts.vcf.gz
vcf2maf		dmp_ACCESS-panelA-v1-isoform-overrides
OncoKB annotate	VEP 105	API token File
MAF annotated By BED/TSV
Mappability BED File	Ensembl HG19	wgEncodeDacMapabilityConsensusExcludable.bed.gz
Complexity BED File	Ensembl HG19	rmsk.txt.gz
47k CHPD TSV File		47K CH Putative Drivers list
Hotspot TSV File		47K CH PD variants with a prevalence >=5
Panmyeloid TSV File		Panmyeloid variants from IMPACT Haeme dataset