CCRGeneticsBranch / khanlab_ngs_pipeline

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Introduction

This is the implementation of KhanLab NGS Pipeline using Snakemake.

Installation

This pipeline is available on NIH biowulf cluster. The data from this pipeline could directly be ported in OncoGenomics-DB, an application created to visualize NGS data available to NIH users.

Requirements

mutt
gnu parallel
SLURM or PBS for resource management
Bioinformatics Tools Listed in config files

Following R Packages

Conventions

DNASeq:

RNASeq:

Patient:

Rulegraph

alt tag

DAG for example Sample alt tag