XhetRel

Introduction

This repository is an analysis pipeline for X heterozygosity and relatedness from exome sequencing VCF files.

How to use

You can either run the Google colab version or run it on your machine. It can be access through the following the link below: https://colab.research.google.com/drive/1ep69JvXLwK5ndHUQ8qIGTWvauzsTW9fi

In order to run it locally you will need nextflow.

./nextflow XhetRel/main.nf --input_dir "$vcf_dir" --output_dir "/content"

VCF files should have AD columns.

Installation

Clone the repo

git clone https://github.com/barslmn/XhetRel

Installing the tools

If you have docker nextflow will automatically fetch the tools required for the analysis.

If you dont have docker installed, you either need to install docker or install the tools manually.

Here how you can do so in a debian based system.

git clone https://github.com/barslmn/XhetRel
curl -s https://get.nextflow.io | bash

pip install git+https://github.com/MultiQC/MultiQC

apt update -y
apt install -y vcftools

apt update -y
apt install -y \
  git gcc zlib1g-dev autoconf make \
  liblzma-dev libbz2-dev libperl-dev \
  libgsl-dev libcurl4-openssl-dev
git clone --branch 1.20 --recurse-submodules https://github.com/samtools/htslib.git
git clone --branch 1.20 https://github.com/samtools/bcftools
cd bcftools
autoheader && autoconf && ./configure --enable-libgsl --enable-perl-filters
make
make install
cd ..
rm -rf bcftools
rm -rf htslib