qingliguo/hmftools

Various algorithms for analysing genomics data

HMF Tools

This repository contains the suite of tools used in the Hartwig Medical Foundation whole genome,targeted DNA and whole transcriptome analysis pipeline.

DNA Pipeline Components

Latest Pipeline Version

The latest HMF pipeline is v5.34. Release notes are here.

The table below has links for the each tool used in this release.

Running the Pipeline

The full pipeline can be run using a NextFlow implmentation called OncoAnalyser.

An example WGS pipeline which runs each of these components in turn is detailed here. An example targeted-panel pipeline, including support for the HMF and TSO-500 panels, is detailed here.

Current versions

Component	Description	Current Version
Amber	Generate a tumor BAF file for Purple's copy number fit	4.0
BamTools	BAM metrics and slicing	1.2
Cider	TCR/BCR V(D)J recombination sequence detection	1.0.3
Cobalt	Determines the read depth ratios for Purple's copy number fit	1.16
Cuppa	Tissue of origin prediction from WGS/WTS	2.0
Gripss	SV filtering	2.4
Lilac	HLA typing	1.6
Linx	SV annotation, clustering & chaining, fusion and disruption calling	1.25
MarkDups	Duplicate marking, consensus reads, UMIs and read unmapping	1.1
Pave	Point mutation annotation and gene impact	1.6
Purple	Estimates copy number, purity and ploidy, and identifies driver events	4.0
Sage	Point mutation variant calling and filtering	3.4
Teal	Measures telomere content and estimates telomeric length	1.2.1
SvPrep	Pre-GRIDSS BAM filtering	1.2

The following external tools are used in the pipeline:

Component	Description	Current Version
GRIDSS	Structural variant calling	2.13.2
Chord	Homologous Recombination Deficiency detection	2.0

Resource files

Resource files for each component (GRCh37 and GRCh38) are available to download from HMFTools-Resources > DNA-Resources.

Actionability and Clinical Reporting Tools

Component	Description	Current Version
Protect	Matching of molecular results to treatments and clinical trials	2.3
Rose	Actionability of clinically relevant molecular findings	1.3
Virus Interpreter	Filtering, annotation and interpretation of virus breakend data	1.3
Orange	PDF summary report and JSON file of all WGS output	3.2.0
Patient-reporter	PDF summary report and JSON file of all clinical relevant WGS output	7.25.1

RNA Tools

Component	Description	Current Version
Isofox	WTS Transcript Abundance, Fusions & Novel Splice Junctions	1.7