Test Parameters

For information about uploading IGV or annotation files, 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. The default pipeline is analysis from FASTQ.
Analysis Pipeline Version	The secondary analysis pipeline version number.
Genome Build	The reference genome assembly used for association.
Sample Classification	The sample type. BaseSpace Variant Interpreter 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. Uploaded files must be in gzip format.

Interpretation

For information about uploading custom IGV or annotation files, 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 (chromosomes 1–22), allosomal (chromosomes X and Y), and mitochondrial (chromosome M) chromosome groups. 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.
Custom Annotations	Additional variant-level annotations to be applied to the case.
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 Categories on page 1.
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. Case managers assign flags in the variant grid. Flags are listed from left to right in order of severity.
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. BaseSpace Variant Interpreter 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.