rnaseq-variant-gatk

Variant calling + processing pipline using GATK based in Snakemake

• Use branch maser for calling with GATK 4
• Use branch gatk37 for calling with GATK 3.7

The GATK4 calling currently does not work due to an issue with how gatk SplitNCigarReads parses its arguments

Usage

source activate [gatk,gatk37] # activate conda enviornment

See here to create the conda environment

snakemake --dag --configfile "XXX-config.yaml" | dot -Tpng > "XXX-worflow.png"
snakemake --configfile "XXX-config.yaml" --cores "N"

Additional parameters can be passed to the Haplotype caller step by way of the hcArgs variable in the config file. For example to restrict genotyping to specific positions on the genome we would add the following line to the config file. (ip provides padding arond each site, recommended by GATK site.)

hcArgs: "-L my_variants.vcf -ip 100"

To do

• Fix GATK 4 calls so it works - is this a bug or implementation issues?

Build process for GATK 4 conda environment

This current process is very much not ideal, but the conda package for gatk4 is not standalone so is unavoidable.

1. Clone the gatk 4 repo

Check if this version is that latest.

wget https://github.com/broadinstitute/gatk/releases/download/4.0.2.1/gatk-4.0.2.1.zip
unzip gatk-4.0.2.1.zip
cd gatk-4.0.2.1.zip

2. Make the conda environment

conda env create -n gatk4 -f gatkcondaenv.yml

3. Add Snakemake and java 1.8 to the conda environment (graphviz is for making snakemake DAGs)

source ~/miniconda/bin/activate gatk4
conda install -c bioconda java-jdk snakemake graphviz

Then update the gatkPath variable in config.yaml with the path to the gatk executable from the gatk downlaod.

Build process for GATK 3.7 conda environment

To use the GATK 3.7 branch follow these instructions to set up the conda environment.

conda create -n gatk37 gatk=3.7
source activate gatk37

Then download version 3.7 of GATK from https://software.broadinstitute.org/gatk/download/archive

gatk-register "/path/to/gatk-XX-tar.bz2"
conda install -c bioconda java-jdk snakemake graphviz