Genome Sequence Informatics

bclconvert

Workflow to process a run directory through Dragen bclconvert

cBioPortal_Importer

Scripts to facilitate loading data into cBioPortal

dimsum

QC Tracking dashboard

djerba

Create cancer bioinformatics reports from metadata and workflow output

shesmu

Decision-driven action launching system

vidarr

Analysis provenance tracking server

dragen-bclconvert

bcl2fastq

Workflow for Illumina's bcl2fastq

ichorCNA

workflow for estimating the fraction of tumour in cell-free DNA from sWGS

bamMergePreprocessing

WDL workflow to filter, merge, mark duplicates, indel realign and base quality score recalibrate groups of related (e.g. by library, donor, project) lane level alignments

bwamem2

workflow for bwa-men2

djerba-demo

Demonstration of the Djerba reporting system

smmipsWorkflow

Workflow for analysis of smMIP libraries

arriba

Fusion caller which runs off of STAR bam

mutect2Consensus

The Mutect2Consensus workflow will process umiConsensus outputs for the tumour data through mutect2 in tumour only mode to call variants then use information from the matched normal to identify likely germline variants.

crosscheckFingerprintsCollector

workflow to generate per library fingerprints for use in gatk CrosscheckFingerprints

mrdetect

workflow to detect Minimal Residual disease with MRDetect

bwaMem

Workflow for BWA mem

bamQC

Workflow to run bam-qc-metrics (https://github.com/oicr-gsi/bam-qc-metrics)

mutect2

Workflow to run Mutect2 (GATK4)

delly

Delly workflow produces a set of vcf files with different types of structural variant calls

variantEffectPredictor

Variant Effect Predictor Workflow

cfMedipsQc

cfMedipsQC workflow produces a set of metrics files for sequencing data generated in methylation profiling of circulating Free DNA.

dellyGermline

Call germline SVs using Delly

tmbAnalysis

A workflow to align fastq reads, call variants, annotate and assess TMB

t1k

dragmap

A workflow to run Dragmap

msisensor

msisensor-pro workflow

hrDetect

Workflow for the sigtools and HRdetect R packages

probeCoverageDistribution

Workflow to calculate probe coverage, calls bwaMem