DNA-SEQ-GATK-VARIANT-CALLING (⚠ FOREIGN IMPORTATION)¶

Version: 1.0.1 Tags: DNA-Seq / Variant Calling / GATK

This Snakemake pipeline implements the [GATK best-practices workflow](https://software.broadinstitute.org/gatk/best-practices/workflow?id=11145) for calling small genomic variants.

You may find more information at:

Github: https://software.broadinstitute.org/gatk/best-practices/workflow?id=11145

Pipeline dependencies¶

This pipeline requires the following packages to be run. Any other additional requirements are being installed dynamically.

Conda:

conda-forge::python=3.7.3

conda-forge::pytest=5.1.2

conda-forge::datrie=0.8

conda-forge::git=2.20.1

conda-forge::jinja2=2.10.1

conda-forge::pygraphviz=1.5

conda-forge::flask=1.1.1

conda-forge::pandas=0.25.1

conda-forge::zlib=1.2.11

conda-forge::openssl=1.1.1c

conda-forge::networkx=2.3

bioconda::snakemake=5.5.4

Additionally, the following prerequisites are non-optional:

Conda
Genome sequence
Known variant sites

Input files¶

Please find below the list of required input files:

Fastq formatted reads (one or multiple ones)
A fasta formatted genome sequence, its index and dictionnary.
A VCF formatted known variant file

Output files¶

Please find below the list of expected output files:

Multiple html reports
VCF files
BAM files

Notes¶

This pipeline comes from the Snakemake workflows: https://github.com/snakemake-workflows/docs

Installation¶

While installing the workflow, you may run the following commands (order matters):

Case

Command line

git

# This command clones the git repository

if [ ! -d "${DNA_SEQ_GATK_VARIANT_CALLING:?}" ]; then git clone https://github.com/snakemake-workflows/dna-seq-gatk-variant-calling.git "${DNA_SEQ_GATK_VARIANT_CALLING:?}"; fi

conda

# This command create conda virtual environment,

# but requires available git repository (see above)

conda env create --force --file "${STRONGR_DIR:?}/workflows/calling/dna-seq-gatk-variant-calling/environment.yaml

Execution¶

In order to execute the pipeline, you may run the following commands:

Case	Command line(s)
local	snakemake --use-conda -pr