A set of CWL tools that are based on scripts used in the OxoGWrapperWorkflow.

Tools contained within:

• check_minibams.sh - Checks that minibams are OK
• clean_vcf.sh - Cleans VCFS so that they are ready to be processed by the OxoGWrapperWorkflow
• normalize.sh - Normalizes INDEL files by calling bcf-tools norm.
• pass_filter.sh - Performs pass-filtering on VCFs.
• vcf_merge_by_type.pl - Merges VCFs.

To get the submodules, use a command like this:

$ git submodule update --init --recursive

You will need the reference files located at https://personal.broadinstitute.org/gsaksena/public_full8.tar.gz

You will need to run the workflow with the cwltool flags --relax-path-checks and --non-strict.