tbWGS

A Nextflow pipeline for post-processing WGS data.

• DRAGEN Germline Calling
• Download the result from Basespace

The pipeline:

1. Annotate small variants from *.hard-filtered.vcf.gz using snpEff and output the variants with high risk for given target regions.
2. Annotate CNV variants from *.cnv.vcf.gz using snpEff and output the variants with high risk for given target regions.
3. Annotate variants from *.sv.vcf.gz using snpEff and output the variants with high risk for given target regions.

Running the pipeline

Run the pipeline with:

nextflow run . --dragen_path <Path download from basespace> --target_bed <bed file>