Test Parameters
For information about uploading files for custom interpretation parameters, see Manage Test Preferences and Files.
Test Details
|
Parameter |
Description |
|---|---|
|
Test Name |
The unique name for the test. Test names cannot be changed. |
|
Test Type |
The test type, as defined by your workgroup. To add a test type, enter a unique test name in the field. |
Analysis
|
Parameter |
Description |
|---|---|
|
Analysis Pipeline |
The secondary analysis to be performed on the sample data. |
|
Analysis Pipeline Version |
The secondary analysis pipeline version number. |
|
Genome Build |
The reference genome assembly used for association. |
|
Sample Classification |
The sample type. TruSight Software supports germline samples only. |
|
QC Threshold |
Thresholds for passing metrics in variant analyses from FASTQ files. |
|
QC Coverage Metrics BED File |
BED file for calculating QC metrics in variant analyses from FASTQ files. A default BED file is included for each version of the reference genome that is based on the Ensemble 26 transcript. Uploaded files must be in gzip format. |
Interpretation
For information about uploading files for custom interpretation parameters, see Manage Test Preferences and Files.
|
Parameter |
Description |
|---|---|
|
Reciprocal Overlap Threshold |
The minimum reciprocal overlap, represented by a value between 0 and 1. Only annotations that meet the minimum overlap for CNVs and SVs are shown in the grid or included in filtering (eg, aggregate population frequency). |
|
Transcript Standard |
The transcript source to be used for autosomal Ensembl—Variants are annotated using Ensembl transcripts. Mitochondrial variants are always annotated using Ensembl. RefSeq—Variants are annotated using RefSeq transcripts. |
|
Phenotype to Genes |
The default parameters for gene lists created by phenotype search. For more information, see Phenotype to Gene Search. Resource—The ontology source for the gene-phenotype relationship. Distance Cutoff—The maximum distance between ontological nodes of linked phenotypes. Values closer to zero indicate that the phenotypes are more equivalent. Confidence—The confidence level for the gene-phenotype relationship. Some phenotype databases include only high confidence relationships. If a filter does not return results, expand the search parameters to include high confidence level. |
|
Custom IGV Files |
Custom BED file with additional tracks for visualization in IGV. Large files must be compressed before upload. |
|
Custom Annotations |
Additional variant-level annotations to be applied to the case. A test can include a maximum of 10 annotation files. |
|
STR Annotation Thresholds |
Custom repeat expansion thresholds. |
Report
|
Parameter |
Description |
|---|---|
|
Report Name |
The unique name for the report. |
|
Report Section List |
A group of reporting categories, as defined by your lab. The report groups variants by the section they are assigned to. For more information, see Using Report Sections. |
|
Report Template |
The template for the PDF report. |
|
Report Label List |
A set of report labels. Case managers assign a label from the list when reviewing the report. |
|
Flag List |
A set of color-coded flags, as defined by your lab. Tests support up to 20 unique flag labels and eight unique colors. |
|
Interpretation Filters |
The saved filters to be applied to the analysis results. In the variant grid, the data for each variant filter is presented in a separate tab. TruSight Software includes preconfigured example filters that illustrate simple filtering scenarios. The filters vary based on the selected genome build. |
|
Test Methodology Note |
Notes about your test methodology. |