Find false negatives by using the variantCaller plugin report

If a hotspots file was used:

1. Check that the position of the variant is included in the hotspots file.

2. Check the Variant Calls output table. Values that cause a candidate to be filtered out are shown in colored cells:

   

3. Adjust plugin parameters.

4. Rerun the variantCaller plugin.

If a hotspots file was not used:

1. Navigate to the variantCaller plugin results directory on the Ion Torrent™ Server and open the small_variants_filtered.vcf file.

   • Open the detailed report in Torrent Suite™ Software, then click the Barcode Name link in a report from a barcoded sequencing run. Or, click the Sample Name link in a report from a non-barcoded sequencing run. Scroll to, or search for the small_variants_filtered.vcf link. You can click the link to view the file in the browser or download the file to your computer.

   • On Linux backend, the variantCaller plugin results directory can be found at /results/analysis/output/Home/{analysis_report_name}/plugins/variantCaller/ for non-barcoded runs or /results/analysis/output/Home/{analysis_report_name}/plugins/variantCaller/{bar code}/ for barcoded runs.

2. Find the location of the variant, then examine the FR (filtered reason) field.

3. Relate the reason to plugin run parameters using the parameter definitions in variantCaller plugin advanced parameters.

4. Adjust plugin parameters.

5. Rerun the variantCaller plugin.