6.2 Choose which workflow to use

VCPA allows user to process either a WGS or WES sample using the latest human reference genome (hg38). For WGS, VCPA provides two options: with or without mapping. Below are the three VCPA workflow options that users can choose from:

• VCPA_WES_hg38_from_mapping_to_variant_call.sh - this is the WES pipeline that includes steps from mapping to variant call using GATK (i.e. steps 0, 1, 2a and 2b in the overview figure in the Introduction session)

• VCPA_WGS_hg38_from_mapping_to_variant_call.sh - this is the WGS pipeline that includes steps from mapping to variant call using GATK (i.e. steps 0, 1, 2a and 2b in the overview figure in the Introduction session)

• VCPA_WGS_hg38_from_markdup_to_variant_call.sh - this is the WGS pipeline that excludes mapping, but includes other steps of VCPA (i.e. steps 1, 2a and 2b in the overview figure in the Introduction session)

Users can choose the workflow by doing this:

cp bin/${PROJECT_WORKFLOW}.sh bin/${PROJECT_WORKFLOW}_aws.sh

PROJECT_WORKFLOW is the one of the three .sh file chosen from the above.