Common mutations in cancer that will be genotyped and passed through into the merged VCF if they have even low-level evidence of a mutation (by default, marked with filter DOCM_ONLY)

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.

bqsr_intervals provides an array of genomic intervals for which to apply GATK base quality score recalibrations. Typically intervals are given for the entire chromosome (chr1, chr2, etc.), these names should match the format in the reference file.

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 reagent. In the case of WGS this generally should contain intervals that span the entire genome.

per_base_intervals is a list of regions (in interval_list format) over which to summarize coverage/QC at a per-base resolution.

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

per_target_intervals list of regions (in interval_list format) over which to summarize coverage/QC at a per-target resolution.

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

custom type, check types directory for input format