A Nextflow pipeline for post-processing WGS data.
- DRAGEN Germline Calling
- Download the result from Basespace
The pipeline:
- Annotate small variants from *.hard-filtered.vcf.gz using snpEff and output the variants with high risk for given target regions.
- Annotate CNV variants from *.cnv.vcf.gz using snpEff and output the variants with high risk for given target regions.
- Annotate variants from *.sv.vcf.gz using snpEff and output the variants with high risk for given target regions.
Run the pipeline with:
nextflow run . --dragen_path <Path download from basespace> --target_bed <bed file>