Upload a file that lists known chromosomal locations with pathogenic variants. Variants that match the whitelist will not be affected by the filtering parameters. Genotype calls for these variants remain exactly as output by the GenomeAnalysisToolkit (GATK) pipeline.
The format of the whitelisted variants file follows the BED file format or the Designer CSV file format for region-based targets. When adding a whitelist file, select *.bed or *.csv at the bottom of the open dialog.
After adding a whitelist file, a Remove all other variants checkbox appears. Select it to remove all variants from the samples that are not in the whitelist.
Only one whitelist file is allowed.
Note: .bed files from the Tapestri Portal Datasets will not work as whitelist files.