MaxGreil / vcftosnp

vcftosnp

Proof of concept of a DNA-Seq pipeline from reads over VCF to SNP (including quality control) with Nextflow.

Prerequisites

• Unix-like OS (Linux, macOS, etc.)
• Java version 8
• Docker engine 1.10.x (or later)

Necessary files

• Reads to be mapped must be stored in compressed .fastq.gz file format in folder data

Additional necessary files

If the reads to be analyzed originate from a human DNA-Seq experiment, this additional file must be stored in folder data:

• Assembly of the human genome (GRCh38 Genome Reference Consortium Human Reference 38)

hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz

Table of Contents

• Quick start
• Installation
• Arguments
• Documentation

Quick start

Installation

Clone this repository with the following command:

git clone https://github.com/maxgreil/vcftosnp && cd vcftosnp

Then, install Nextflow by using the following command:

curl https://get.nextflow.io | bash

The above snippet creates the nextflow launcher in the current directory.

Finally pull the following Docker container:

docker pull maxgreil/vcftosnp

Alternatively, you can build the Docker Image yourself using the following command:

cd docker && docker image build . -t maxgreil/vcftosnp

Arguments

Optional Arguments

Argument	Usage	Description
--reads	<files>	Directory and glob pattern of input files
--outdir	<folder>	Directory to save output files

Documentation

Pipeline overview

The pipeline is built using Nextflow and processes data using the following steps: