Variants that pass all the set filters are reported to a single output VCF file and all variants that fail any one of the set filters are reported to a filtered output VCF file. The filtered variants have an associated filter reason tag in the VCF file, which the users can query to identify the filters that the candidate variant failed to pass.

The following reports are also available in tab-separated format:

• The Variant Calls table
• Hotspot Alleles table
• The Classic output table

Output from the variantCaller plugin includes the following reports and sections:

• Run report plugin summary

• Variant Caller Report

• Variant Caller Report summary section

• Variant Caller Report Variant Calls table