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 --recursiveYou 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.