Translational Genomics Research Institute

banovichlab

Public code repository for the Banovich Lab at the Translational Genomics Research Institute (TGen).

CovGen

Creates a target specific exome_full192.coverage.txt file required by MutSig

MMRF_CoMMpass

A collection of scripts used to recreate files and graphs used in the MMRF CoMMpass analysis.

bisbee

alternative splicing analysis pipeline

phoenix

Jetstream compatible workflow template supporting comprehensive analysis of human sequencing data against GRCh38

jetstream

Workflow management system written as a pure Python package and command-line utility. It supports complex workflows modeled as directed- acyclic graphs (DAGs), and execution on batch schedulers

lumosVar2

Calls somatic SNVs, indels, and allelic copy number jointly across multiple samples from the same patient. These can be standard tumor/normal pair, longitudinal samples, primary/met, etc. Can also be used for tumor only calling, ideally with a high tumor content and a low tumor content sample.

vcfMerger2

Dynamic vcfMerger for 2 to N somatic variants vcf files

Institutional_Instructions

Description of institutional rules and regulations regarding the usage of github, plus usage guidelines

jetstream_resources

Collection of scripts and README files tracking the source and generation of reference genomes and annotation files

ppmi-qc-wt-paper

QC of whole blood whole transcriptome for PPMI

gvm

Replacement for LumosVar preprocess step

ppmi-rnaseq-wb-paper

code used to generate figures for the ppmi whole blood rnaseq paper

coyote

GemDb

GemDb mongo variants/annotations hub

pegasusPipe

Post_Medusa_Processing

tempe

A container focused and streamlined iteration of the Phoenix pipeline

MARS

Check the purity of a multiple myeloma tumor sample with this tool.

snpSniffer

Tool for checking genotype concordance between multiple assays

containers

docker_factory

Create docker images from scratch

GemDb37

Variant database for human genome build 37, includes public annotations and various TGen projects.

GemDb38

gencode-plus-lncipedia

non-redundant genome annotation combining GENCODE 29 and lncipedia 5.2

ichorCNA

Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.

jetstream_containers

Containers for running TGen Jetstream pipelines

Keats_Lab_Public

Public resources from the Keats Lab at TGen

manta

Structural variant and indel caller for mapped sequencing data

tgen-jetstream-docs