Commands and Modules used by the Reference Improvement group.
Pilot test for using the Arvados system to create new MGI cancer pipelines.
Web client for CIViC: Clinical Interpretations of Variants in Cancer
Core modules used by the GMS
Docker containerization for the CLE
Rich Transactional Objects for Perl
Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.
Rails frontend to The Genome Institute's drug gene interaction database.
Backend Server for CIViC Project
Docker for Running Sqitch with MySQL on Trusty at MGI
A full featured, including pull requests, git repo for the arvados_trial Wiki
count DNA sequence reads in BAM files
R package that uses a variational Bayesian approach to fitting a mixture of Beta distributions
An R package for inferring the subclonal architecture of tumors
Washington University Genome Center Hudson testing suite and deploy scripts
Docker File for Running 10X Genomics Long Ranger Aligner
10X Genomics Cell Ranger Suite for Docker!
Graphite Config and Cron Scripts
Docker image for bcl2fastq2
Combination varscan/samtools container for easier running in workflows.
Docker containerization for Ensembl Variant Effect Predictor
Variant of vep image without an ENTRYPOINT
Beautiful static documentation for your API
A wrapper for the docker-strelka image for use in CWL-based workflows.
A docker image for Strelka
Repo for advertising and organizing CIViC hackathon/meeting activities
For CIViC curation issues that do not directly involve code changes
pindelsomaticfilter docker container for cwl