Annotation parameters

You can modify the following annotation parameters to optimize analysis results when you create or edit Ion Reporter™ Software analysis workflows.

IMPORTANT! Use the default parameter settings unless you are an advanced user.


Parameter	Description
Main tab
Analysis options
Functional Annotations For All Alleles	Flag to include functional annotations for genotype-positive alleles only (false) or all reported alleles (true) for variants. Allowed values: True or False
Use IUPAC Single Letter Code for Amino Acid	Use True for IUPAC single letter code for amino acid. Use False for three letter code. Allowed values: True or False
Annotation Statistics and Reporting General Options
dbSNP Hit Level	Flag to control specificity of dbSNP annotations. 'overlap' matches all annotations whose loci overlap with variant. 'locus' matches all annotations whose loci start at variant locus. 'allele' matches all annotations that are 'locus' matches plus have at least one allele in common with variant. 'auto' hit level matches the most specific hit level possible to the annotation which can be any of the overlap, locus, allele or genotype hit levels. Allowed values: overlap locus allele auto
ClinVar Hit Level	Flag to control specificity of ClinVar annotations. 'Overlap' matches all annotations whose loci overlap with variant. 'Locus' matches all annotations whose loci start at variant locus. 'Allele' matches all annotations that are 'locus' matches plus have at least one allele in common with variant. 'Auto' hit level matches the most specific hit level possible to the annotation which can be any of the overlap, locus, allele or genotype hit levels. Allowed values: overlap locus allele auto
COSMIC Hit Level	Flag to control specificity of COSMIC annotations. 'Overlap' matches all annotations whose loci overlap with variant. 'Locus' matches all annotations whose loci start at variant locus. 'Allele' matches all annotations that are 'locus' matches plus have at least one allele in common with variant. 'Auto' hit level matches the most specific hit level possible to the annotation which can be any of the overlap, locus, allele or genotype hit levels. Allowed values: overlap locus allele auto
VariantDB Hit Level	Flag to control specificity of VARIANTDB annotations. 'Overlap' matches all annotations whose loci overlap with variant. 'Locus' matches all annotations whose loci start at variant locus. 'Allele' matches all annotations that are 'locus' matches plus have at least one allele in common with variant. 'Genotype' matches all annotations that are 'allele' matches where the genotypes also match. 'Auto' hit level matches the most specific hit level possible to the annotation which can be any of the overlap, locus, allele or genotype hit levels. Allowed values: overlap locus allele auto
ExAC Hit Level	Flag to control specificity of ExAC annotations. 'Overlap' matches all annotations whose loci overlap with variant. 'Locus' matches all annotations whose loci start at variant locus. 'Allele' matches all annotations that are 'locus' matches plus have at least one allele in common with variant. 'Auto' hit level matches the most specific hit level possible to the annotation which can be any of the overlap, locus, allele or genotype hit levels. Allowed values: overlap locus allele auto
Gene Extension Size	Gene extension is the number of bases upstream and downstream of the start and end positions in a transcript that should include the regulatory and control regions. Allowed values: 0 to unlimited
Splice Site Size	The 5' splice site of an exon is the small intronic region immediately upstream, which depends on the strand. Its size in bases is given by splice site size. Allowed values: 0 to unlimited Suggested trial value: 2
Tumor Mutational Burden tab
Tumor Mutational Burden Filter Chain	Filters out the potential germline variants and retains the somatic variants for tumor mutational burden calculation after the variant calling and variant annotation is complete for the analysis. To enable tumor mutational burden calculations on DNA samples, you must also edit, or copy and edit, either: any DNA–Single Sample, or DNA and Fusions–Single Sample analysis workflow. For more information, see Enable tumor mutational burden calculation in existing analysis workflows. To enable the tumor mutational burden calculation for any other analysis workflow, you must select an available filter chain options. Allowed values: TMB (Non-germline Mutations). If you use an analysis workflow for a Tumor Mutation Load Assay, TMB (Non-germline Mutations) is selected by default. Mutation Load (Somatic Mutations) More user-defined filter chains (if created on the server) IMPORTANT! Do not enable the filter chain parameter for other workflow types other than a DNA–Single Sample, or DNA and Fusions–Single Sample analysis workflow.
Tumor Mutational Burden Calculation Version	The version of the tumor mutational burden algorithm that is available in the software is listed. The algorithm version can provide information about how the data was analyzed and can be useful if earlier versions of the software were used, or for troubleshooting.
Minimum Base Coverage	The minimum depth of base coverage required for a variant to be counted for TMB calculation. Allowed values: 0 to unlimited
TMB Variant Minimum Allele Frequency	The minimum alternate allele frequency for a variant to be included for TMB calculation. Allowed values: 0 to 1 You can use this parameter to reduce the affect of deamination in low-quality FFPEs and obtain a higher minimum allele frequency for a tumor mutational burden calculation. For more information, see Reduce the impact of deamination in low-quality FFPEs.
TMB Variant Region Type	The type of region to include for TMB calculation. Allowed values: Exonic regions only Total target regions (exonic + intronic regions)
TMB Variant Type	The variant types to be included for TMB calculation. Allowed values: SNV INDEL MNV
TMB Variant Effect Type	The variant effect types to be included for TMB calculation. Allowed values: missense frameshiftDeletion frameshiftInsertion nonframeshiftDeletion nonframeshiftInsertion nnsense stoploss synonymous unknown
Deamination QC Threshold	The deamination value above which a sample is deemed failed for TMB reporting. Allowed values: 0 to unlimited
Calibration Minimum Cutoff	The lower limit of the range at which the germline calibration is applied. Allowed values: 0 to unlimited
Calibration Maximum Cutoff	The upper limit of the range at which the germline calibration is applied. Allowed values: 0 to unlimited
TMB Germline-Filter Calibration Factor: Slope	The user-supplied value for the slope of the linear curve to which the number of somatic variants is calibrated. Allowed values: 0 to unlimited
TMB Germline-Filter Calibration Factor: Intercept	The user-supplied value for the intercept of the linear curve to which the number of somatic variants is calibrated. Allowed values: −2,000 to 2,000
TMB-Low Threshold	The TMB (mut/mb) threshold below which a sample is defined as TMB-Low. Allowed values: 0 to unlimited
TMB-High Threshold	The TMB (mut/mb) threshold above which a sample is defined as TMB-High. Note: A TMB score that is above the TMB-Low Threshold and below the TMB-High Threshold is defined as Intermediate.
TMB Standardization	Apply the standardization of the observed TMB value to fit a linear curve. Allowed values: On or Off
TMB Standardization Factor: Slope	The user-supplied value for the slope of the linear curve to which the observed final TMB value is adjusted. Allowed values: 0 to unlimited
TMB Standardization Factor: Intercept	The user-supplied value for the intercept of the linear curve to which the observed final TMB value is adjusted. Allowed values: -2,000 to 2,000