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Rajesh Patidar edited this page Sep 8, 2016 · 3 revisions

Introduction

This is the implementation of KhanLab NGS Pipeline using Snakemake.

Installation

The easiest way to get this pipeline is to clone the repository.

git clone https://github.com/patidarr/ngs_pipeline.git

Conventions

  • Sample names cannot have "/" or "." in them
  • Fastq files end in ".fastq.gz"
  • Fastq files are stored in DATA_DIR (Set as Environment Variable)

DNASeq:

  • QC
  • BWA, Novoalign
  • Broad Standard Practices on bwa bam
  • Haplotype Caller, Platupys, Bam2MPG, MuTect, Strelka
  • snpEff, Annovar, SIFT, pph2, Custom Annotation
  • Coverage Plot, Circos Plot, Hotspot Coverage Box Plot

RNASeq:

  • QC
  • Tophat, STAR
  • Broad Standard Practices on STAR bam
  • fusion-catcher, tophat-fusion, deFuse
  • Cufflinks (ENS and UCSC)
  • Haplotype Caller
  • snpEff, Annovar, SIFT, pph2, Custom Annotation
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