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ace

Absolute Copy number Estimation using low-coverage whole genome sequencing data

acquacotta-shiny-run-report

Interactive and dynamic representation of SeqWare Run Reports

analysis_reports

for generation of analysis reports to accompany released data

analysisprocedures

anonymize_report

A script to anonymize release reports

arriba

Fusion caller which runs off of STAR bam

arribatomavis

Convert Arriba output to Mavis format

artic-ncov2019

ARTIC nanopore protocol for nCoV2019 novel coronavirus

bam-qc-metrics

Metrics for BAM file QC

bam-statistics

Scripts that generate statistics for BAM files

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

bamqc

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

bamqc-legacy

Perl scripts for generating quality control stats from BAM files

bamtofastq

Generate R1 and R2

barcodex

barcodex-rs

Reimplementation of barcodex for performance

bcl2barcode

bcl2fastq

Workflow for Illumina's bcl2fastq

bis-utils

This repo contains scripts that are routinely used for BIS team

bwamem

Workflow for BWA mem

bwamem2

workflow for bwa-men2

calculatecontamination

A WDL workflow that runs GATK4 CalculateContamination from FastQ files.

callability

cardea

Case data API

cbioportal_importer

Scripts to facilitate loading data into cBioPortal

cbioportal_tools

tools for import of data and administration of the gsi cbioportal instance

cbiowrap-workflow

cellrangerataccount

cellrangercount

WDL Workflow to run cellranger count

cellrangerdnacnv