Annotation parameters
You can modify the following annotation parameters to optimize your 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 |
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Flag to include functional annotations for genotype-positive alleles only (false) or all reported alleles (true) for variants. |
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Use True for IUPAC single letter code for amino acid. Use False for three letter code. |
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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 could be any of the overlap, locus, allele or genotype hit levels. |
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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 could be any of the overlap, locus, allele or genotype hit levels. |
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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 could be any of the overlap, locus, allele or genotype hit levels. |
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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 could be any of the overlap, locus, allele or genotype hit levels. |
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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 could be any of the overlap, locus, allele or genotype hit levels. |
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Gene extension is the number of bases upstream and downstream of a transcript's start and end positions that should include the regulatory and control regions. |
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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 Note: Prior to Ion Reporter™ Software 5.10, we defined splicesite_5 and splicesite_3 as exon-centric. This was contrary to the common convention of splice site nomenclature that was intron-centric and would exchange the splicesite_5 and splicesite_3 designations. In Ion Reporter™ Software 5.10, splicesite_5 and splicesite_3 refers to the intron locations. In earlier releases of the software, you might have seen a 3' splice site in your results; you will now see a 5' splice site and vice versa. |
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Filters out the potential germline variants and retains the somatic variants for tumor mutational burden calculation after the variant calling and variant annotation is completed 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 one of the available filter-chain options.
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. |
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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 in the case of troubleshooting. |
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The minimum depth of base coverage required for a variant to be counted for TMB calculation. |
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The minimum alternate allele frequency for a variant to be included for TMB calculation. You can use this parameter to reduce the affect of deamination in low-quality FFPEs and achieve a higher minimum allele frequency for a tumor mutational burden calculation. For more information, see Reduce the impact of deamination in low-quality FFPEs. |
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The type of region to include for TMB calculation. |
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The variant types to be included for TMB calculation. |
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The variant effect types to be included for TMB calculation. |
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The deamination value above which a sample is deemed failed for TMB reporting. |
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The lower limit of the range at which the germline calibration is applied. |
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The upper limit of the range at which the germline calibration is applied. |
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The user-supplied value for the slope of the linear curve to which the number of somatic variants will be calibrated. |
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The user-supplied value for the intercept of the linear curve to which the number of somatic variants will be calibrated. |
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The TMB (mut/mb) threshold below which a sample is defined as TMB-Low. |
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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. |
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Apply the standardization of the observed TMB value to fit a linear curve. |
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The user-supplied value for the slope of the linear curve to which the observed final TMB value will be adjusted. |
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The user-supplied value for the intercept of the linear curve to which the observed final TMB value will be adjusted. |
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