sequence represents the sequencing data as either FASTQs or BAMs with accompanying readgroup information. Note that in the @RG field ID and SM are required.

array of plugins to use when running vep

bait_intervals is an interval_list corresponding to the baits used in sequencing reagent. These are essentially coordinates for regions you were able to design probes for in the reagent. Typically the reagent provider has this information available in bed format and it can be converted to an interval_list with Picard BedToIntervalList. Astrazeneca also maintains a repo of baits for common sequencing reagents available at https://github.com/AstraZeneca-NGS/reference_data

One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis.

target_intervals is an interval_list corresponding to the targets for the capture reagent. Bed files with this information can be converted to interval_lists with Picard BedToIntervalList. In general for a WES exome reagent bait_intervals and target_intervals are the same.

ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus

ensembl version - Must be present in the cache directory. Example: 95

genome assembly to use in vep. Examples: GRCh38 or GRCm38

custom type, check types directory for input format

The effective coverage of capture products generally extends out beyond the actual regions targeted. This parameter allows variants to be called in these wingspan regions, extending this many base pairs from each side of the target regions.