Genomic Data Analysis II

Variant Calling Container

Below are the resources required to construct a variant calling container. I have included several extra variant calling tools in the container (Strelka, Mantra, Google DeepVariant, GATK, FreeBayes) as some of you might want to try different variant calling tools for your thesis project.

Jump to

yml

name: Germline_VC
channels:
  - bioconda
  - conda-forge
  - defaults
  - agbiome
dependencies:
  - agbiome::bbtools
  - conda-forge::markdown=3.1.1
  - conda-forge::pymdown-extensions=6.0
  - conda-forge::pygments=2.5.2
  - bioconda::ascat=2.5.2
  - bioconda::bcftools=1.9
  - bioconda::bwa=0.7.17
  - bioconda::cancerit-allelecount=4.0.2
  - bioconda::cnvkit=0.9.6
  - bioconda::control-freec=11.5
  - bioconda::ensembl-vep=99.2
  - bioconda::fastqc=0.11.9
  - bioconda::freebayes=1.3.2
  - bioconda::gatk4-spark=4.1.7.0
  - bioconda::genesplicer=1.0
  - bioconda::htslib=1.9
  - bioconda::manta=1.6.0
  - bioconda::msisensor=0.5
  - bioconda::multiqc=1.8
  - bioconda::qualimap=2.2.2d
  - bioconda::samtools=1.9
  - bioconda::snpeff=4.3.1t
  - bioconda::strelka=2.9.10
  - bioconda::tiddit=2.7.1
  - bioconda::trim-galore=0.6.5
  - bioconda::vcfanno=0.3.2
  - bioconda::vcftools=0.1.16
  - conda-forge::pigz=2.3.4
  - conda-forge::r-ggplot2=3.3.0
  - conda-forge::pip=10.0.1
  - bioconda::deepvariant=0.10.0
  - bioconda::picard=2.18.7
  - conda-forge::lbzip2=2.5
  - conda-forge::google-cloud-sdk<243.0.0

Dockerfile

FROM nfcore/base:1.9
LABEL authors="Barry Digby" \
      description="Docker image containing all software requirements for Germline Variant Calling Analysis"

# Install the conda environment
COPY environment.yml /
RUN conda env create -f /environment.yml python=2.7.15 && conda clean -a

# Add conda installation dir to PATH (instead of doing 'conda activate')
ENV PATH /opt/conda/envs/Germline_VC/bin:$PATH

# Dump the details of the installed packages to a file for posterity
RUN conda env export --name Germline_VC > Germline_VC.yml

Singularity

You can create the image yourself and push to your own dockerhub account or you can download it from my dockerhub account.

singularity pull --name germline_vc.img docker://barryd237/germline_vc:latest