DNAvc pipeline

a DNA variant calling pipeline from indexed .bam files to .vcf files with stats report.

(DeepVariant currently optimised for Illumina WGS)

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set up pipeline

before running, you have to set up the attached Docker image which includes OpenCRAVAT and 2 others (all will take quite some time and overall need >50 GB of memory, you can add/remove OpenCRAVAT modules according to your needs in the Dockerfile, currently adapted for breast cancer):

docker build -t dnavc-pipeline https://raw.githubusercontent.com/loipf/DNAvc-pipeline/master/docker/Dockerfile
docker pull google/deepvariant:1.2.0
docker pull quay.io/mlin/glnexus:v1.2.7

now either replace the Docker container hash (last output line from previous build command) in nextflow.config or run nextflow with the -with-docker dnavc-pipeline argument.

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run mapping pipeline

it can be run locally with downloaded github-repo and edited nextflow.config file with:

nextflow run main.nf

or

nextflow run loipf/DNAvc-pipeline -r v1.0 --project_dir /path/to/folder --reads_mapped_dir /path/to/samples --reference_genome /path/to/ref --num_threads 10 -with-docker dnavc-pipeline

for this execution to work properly, you have to be in the current project directory.

optional extendable with:

-resume
-with-report report_DNAseq-pipeline
-with-timeline timeline_DNAseq-pipeline
-w work_dir

by default, all output will be saved into the data folder of the current directory. mapped .bam files must already be indexed.