Tools Description
Versions of tools in order of process
Tool | Version |
1.8.2 | |
0.1.5 | |
1.15.1 | |
1.6 | |
5.0 | |
1.6.21 | |
3.2.2 | |
0.2.3 | |
0.2.3 | |
0.2.3 | |
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 |
Last updated