oicr-gsi Goto Github PK
Name: Genome Sequence Informatics
Type: Organization
Bio: Repositories for OICR's Genome Sequence Informatics team
Location: Toronto, ON
Name: Genome Sequence Informatics
Type: Organization
Bio: Repositories for OICR's Genome Sequence Informatics team
Location: Toronto, ON
Workflow for FastQC
Release information for each run and project for fastqs sequenced at OICR
Create "haplotype maps" of variants in order to use with Picardtools Crosscheck_Files utility, which allows for robust genotyping of functional genomic data.
projectconfig UI
freec workflow - call CNV on your tumor wih optional normal
Toolkit for benchmarking fusion transcript predictions
Genotype GVCFs WDL workflow for GATK4
Haplotype caller WDL workflow for GATK4
OICR WDL implementation of GRIDSS PURPLE LINX
Config files for setting up new developers in GSI
Libraries for making the GSI website
Reporting repository and report record keeping
workflow wraps HLA-VBSeq, a tool for estimating the most prevalent HLA types in a sample
wrapper workflow for BCGSC tool HLAminer
Calls Copy Number Variants on sequencing data from cancer patients
common Fingerprint Collector workflow, that aligns sequence and runs 1 or more sample fingerprinting tools
Workflow for the sigtools and HRdetect R packages
Workflow to run HSMetrics
workflow for estimating the fraction of tumour in cell-free DNA from sWGS
Workflow to run immunedeconv functions
workflow for indel validation, based on CGI-Tools/6-indelValidate.sh
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