Loading...
Versions of tools in order of process
Tool
Version
1.8.2
0.1.5
1.15.1
1.6
Files and Resources used
There are multiple files from different resources used in this workflow.
Mappability BED File
Ensembl HG19
wgEncodeDacMapabilityConsensusExcludable.bed.gz
Complexity BED File
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
SnpSift - annotatearrow-up-right
5.0
vcf2mafarrow-up-right
1.6.21
OncoKB - annotatorarrow-up-right
3.2.2
Post Processing Variant - MAF annotated by BEDarrow-up-right
0.2.3
Post Processing Variant - MAF annotated by TSVarrow-up-right
Post Processing Variant - MAF tagarrow-up-right
Post Processing Variant - MAF filterarrow-up-right
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