Predefined filter chains

Ion Reporter™ Software includes predefined filter chains that you can apply to analysis workflows, analysis results, or visualizations. Filter chains are sets of filters that Ion Reporter™ Software uses to narrow the list of variants that are included in analysis results. The filter chains are based on public and proprietary annotation sources and data types that are included in Ion Reporter™ Software. For more information, see Annotation source filters and Data type filters.

You cannot edit predefined filter chains, but you can create custom filter chains that are built from predefined filter chains, or from one or more filters. For more information, see Create a custom filter chain.

Predefined filter chain name

Description

AmpliSeq Exome Tumor Normal v1

This filter chain detects all CNVs, confident somatic variants with allele ratios between 0.1 and 1.0, allele read counts between 4 and 1,000,000, and PValue between 0 and 5.0E-6.

This is the default filter chain for Ion AmpliSeq™ Exome tumor-normal pair analysis workflows. The confidence range is 10.0 to 1.0E7.

Aneuploidy Mosaicism

This filter chain detects mosaicism by allowing decimal-level copy number gain or loss calls with a confidence score of at least 0.1, while filtering out false positive calls near expected normal copy number.

This filter chain is turned on by default in the ReproSeq Mosaic PGS w1.1 analysis workflow, and is not selected by default in other predefined aneuploidy analysis workflows.

Called Hotspot Variants and Controls

This filter chain reports all hotspot variants that pass the filter and are not called as reference or NOCALL. Variant types include SNP and INDEL.

This filter chain displays the same set of variants in the Analysis Results view as in the SNP/INDEL summary table in visualization view.

Called Variants and Controls

This filter chain reports all variants (either hotspots or novel) that pass the filter and are not called as reference or NOCALL.

Variant types include SNV, INDEL, MNV, CNV, LONGDEL, FUSION, EXPR_CONTROL, ASSAYS_5P_3P, RNA_HOTSPOT, GENE_EXPRESSION, RNAExonVariant, ProcControl, and FLT3ITD.

CNVs of Confidence ≥0.1–Germline–CNVs only

For germline analyses, this filter chain narrows your analysis results to copy number variants with a confidence value of ≥0.1.

Confident CNVs—CNVs Only

This filter chain returns the variants whose minimum ploidy gain (5% CI) is over expected, which is 1.0, OR minimum ploidy loss (95% CI) is under expected, which is also 1.0.

Confident Germline CNVs–CNVs Only

For germline analyses, this filter chain narrows your analysis results to copy number variants with a confidence value of ≥10.

Not a default filter.

Confident Somatic CNVs–CNVs Only

This filter chain includes 5% confidence interval range and 95% confidence interval range.

Filter chain logic

10.0 <= CNV Confidence Range <= 1.0E7

Default CarrierSeq View

This is the default filter chain for CarrierSeq analysis workflows. It filters out all of the reference calls and displays the others that are relevant to genotypes and CNVs.

For more information, see Ion Torrent™ CarrierSeq™ ECS Kits User Guide, Pub. No. MAN0018483.

Filter chain logic

Variant Type in [MNV, SNV, INDEL, NOCALL] OR (Variant Type in CNV AND Filter in [GAIN, LOSS, NOCALL])

Default DNA and Fusions View

This is the default filter chain for the Ion AmpliSeq™ Colon Lung v2 with RNA Lung Fusion single-sample analysis workflow. Either fusion detection is present, or the variant type is not fusion.

Results include:

  • FUSIONS variants detected as Present

  • All EXPR_CONTROL markers

  • All ASSAYS_5P_3P markers

  • DNA variants of all types

Default Fusions View

This is the default filter chain for the Ion AmpliSeq™ RNA Lung fusion single-sample analysis workflow.

Either fusion detection is present, or the variant type is:

  • EXPR_CONTROL

  • ASSAYS_5P_3P

  • RNA_HOTSPOT

  • GENE_EXPRESSION

Default Variant View

This is the default filter chain for the following analysis workflows:

  • Ion AmpliSeq™ Exome single-sample (both Germline and Somatic)

  • TargetSeq Exome v2 single-sample

  • Ion AmpliSeq™ CHPv1 tumor-normal pair

  • Ion AmpliSeq™ CHPv2 tumor-normal pair

  • Ion AmpliSeq™ CCP tumor-normal pair

  • Ion AmpliSeq™ Exome paired sample

  • Ion AmpliSeq™ CCP paired sample

  • non-ReproSeq Low-pass whole-genome aneuploidy

This filter chain narrows your analysis results to confident variant types, which are not CNVs, but could include SNV, INDEL, MNV, REF, NOCALL, LONGDEL, FUSION, EXPR_CONTROL, ASSAYS_5P_3P, RNA_HOTSPOT, GENE_EXPRESSION, RNAExonVariant, ProcControl, and FLT3ITD.

Genetic Disease Variants

This filter chain narrows your analysis results to genetically-relevant variant types: IsNewlyHomozygousNonRef, HasDeNovoNonRefAllele, HasUnknownX, InTransPhaseCompoundHeterozygote, and HasMaleMaternalX.

This is the default filter chain for the Ion AmpliSeq™ Exome trio and Ion AmpliSeq™ IDP trio analysis workflows.

Mutation Load (Somatic Mutations)

This filter chain is for use only with Ion Reporter™ Software 5.10 analysis workflows.

Mutation Load (Somatic SNVs)

This filter chain returns results for somatic SNVs based upon dbSNP, 5000Exomes, ExAC, and UCSC Common SNPs annotation source databases. The minor allele frequencies range lies between 0.0 and 1.0E-6.

This filter chain also filters out variants of homopolymer lengths greater than 7, coverage lower than 60, and allele frequency less than 0.05.

The Tumor Mutational Burden Filter Chain parameter for this filter chain must be enabled for Ion Reporter™ Software to generate mutation load analysis results. By default, the tumor mutational burden calculation is disabled. You must also copy and edit either a DNA–Single Sample analysis workflow or a DNA and Fusions–Single Sample analysis workflow to enable mutation load calculations on DNA samples.

Filter chain logic

(Filtered Coverage >= 60) AND (Variant Type in SNV) AND (0.0 <= Minor Allele Frequency <= 1.0E-6) AND (0.0 <= 5000Exomes Global MAF <= 1.0E-6) AND (0.0 <= ExAC GAF <= 1.0E-6) AND (UCSC Common SNPs = Not In) AND (0 <= Homopolymer Length <= 7) AND (0.05 <= Allele Frequency <= 1.0)

This filter chain is for use only with Ion Reporter™ Software 5.10 analysis workflows.

Oncomine™ BRCA

This is the default filter chain for Oncomine™ BRCA analysis workflows. It removes any variants in the sample ID amplicons that are not in the BRCA1 and BRCA2 genes.

Oncomine™ Extended

This filter chain includes all Oncomine™-annotated variants and variants that may be relevant to cancer due to their inclusion in one or more of the following classes:

  • Nontargeted fusions.

  • Likely somatic mutations based upon dbSNP, 5000Exomes, ExAC, and UCSC Common SNPs annotation source databases. The minor allele frequencies range lies between 0.0 and 1.0E-6. Mutations must also be nonsynonymous and occur in exonic or splice-site regions.

  • Variants with ClinVar annotations of pathogenic or likely pathogenic.

Filter chain logic. Note that *** means that the Include Unannotated Variants option was checked:

Oncomine = IN

OR

(Variant Type in FUSION AND Filter in PASS)

OR

(Variant Type in SNV, INDEL, MNV, LONGDEL AND

0.0 <= Minor Allele Frequency*** <= 1.0E-6 AND

0.0 <= 5000Exomes Global MAF(20161108)*** <= 1.0E-6 AND

0.0 <= ExAC GAF(1)*** <= 1.0E-6 AND

UCSC Common SNPs = "Not In" AND

Variant Effect in missense, frameshiftDeletion, frameshiftInsertion, nonframeshiftDeletion, nonframeshiftInsertion, nonsense, nonframeshiftBlockSubstitution, frameshiftBlockSubstitution, stoploss AND

Location in exonic, splicesite_3, splicesite_5)

OR

ClinVar(20180729) in

"Pathogenic",

"Likely pathogenic",

"Pathogenic/Likely pathogenic",

"Pathogenic, other",

"Uncertain significance,Likely pathogenic",

"Pathogenic,Conflicting interpretations of pathogenicity",

"Pathogenic,Uncertain significance",

"Pathogenic,Likely pathogenic",

"Conflicting interpretations of pathogenicity,Likely pathogenic",

"Pathogenic,other",

"Pathogenic,Benign",

"Pathogenic,Pathogenic/Likely pathogenic",

"Likely pathogenic, drug response",

"Pathogenic,Benign/Likely benign",

"Pathogenic/Likely pathogenic, drug response",

"Pathogenic,not provided",

"Pathogenic, risk factor",

"Pathogenic, Affects",

"Likely pathogenic, risk factor",

"Pathogenic/Likely pathogenic, risk factor",

"Pathogenic, other, risk factor",

"Likely pathogenic, association",

"Pathogenic, protective",

"Pathogenic,Conflicting interpretations of pathogenicity, other,Benign",

"Pathogenic,Conflicting interpretations of pathogenicity,Likely pathogenic",

"Pathogenic, protective, risk factor",

"Pathogenic/Likely pathogenic, other",

"Likely pathogenic, other",

"Pathogenic,Conflicting interpretations of pathogenicity,Uncertsignificance",

"Pathogenic,Likely benign",

"Pathogenic,Conflicting interpretations of pathogenicity, risk factor",

"Pathogenic,other,association",

"Pathogenic,drug response",

"Pathogenic,Conflicting interpretations of pathogenicity, other",

"Pathogenic/Likely pathogenic,Likely pathogenic",

"Pathogenic,Pathogenic, other",

"Pathogenic/Likely pathogenic, risk factor,Pathogenic",

"Pathogenic, drug response",

"Benign,Likely pathogenic",

"Benign/Likely benign,Likely pathogenic",

"Pathogenic,Conflicting interpretations of pathogenicity, other,other",

"Pathogenic,Conflicting interpretations of pathogenicity, rfactor,Likely pathogenic",

"Pathogenic, association, protective",

"Pathogenic,Benign,Pathogenic/Likely pathogenic",

"Benign,Pathogenic/Likely pathogenic"

Oncomine™ Variants

This filter chain returns results for INDELs and SNV variant types, and minor allele frequencies between 0.0 and 1.0E-6 based on 5000Exomes and ExAC annotation source databases that have homopolymer lengths less than or equal to 7 and allele frequencies between 0.05 and 1.0.

Oncomine™ Variants, 5% CI CNV ploidy ≥gain of 2 over normal

This filter chain restricts copy number variants to gains of greater than 2 based on the 5% confidence interval level. It also returns Oncomine™-annotated variants.

TMB (Non-germline Mutations)

This filter chain returns results for somatic variants based upon dbSNP, 5000Exomes, ExAC, and UCSC Common SNPs annotation source databases. The minor allele frequencies range is between 0.0 and 1.0E-6. This filter chain also filters out variants of homopolymer lengths greater than 7.

The Tumor Mutational Burden Filter Chain parameter for this filter chain must be enabled for Ion Reporter™ Software to generate tumor mutational burden analysis results. By default, tumor mutational burden calculation is disabled. You must also copy and edit either a DNA-Single Sample or a DNA and Fusions-Single Sample analysis workflow to enable tumor mutational burden calculations on DNA samples. Unlike other Ion Reporter™ Software filter chains, the TMB (Non-germline Mutations) filter chain generates final analysis results, and cannot be used to change the variants that are included in the analysis results. That is, tumor mutational burden results that are generated though the use of this filter chain cannot be changed after an analysis is complete.

The filter chain is applied prior to the parameter application. The filtered variant file is passed to the TML script that further applies the user parameters.

Filter chain logic

(0 <= Homopolymer Length <= 4) AND (0.0 <= Minor Allele Frequency <= 1.0E-6) AND (0.0 <= 5000 Exomes Global MAF <= 1.0E-6) AND (0.0 <= ExAC GAF <= 1.0E-6) AND (UCSC Common SNPs = Not In)

Variant Matrix Summary

For visualizations that include the Variant Matrix, such as TagSeq and Ion AmpliSeq™ HD analyses, this filter chain returns results in a visualization that contains the same set of variants that are included in the Variant Matrix Summary tab.

This filter chain allows results to be exported. Import the exported results file into Oncomine™ Reporter (OKR) to include the variants shown in the Variant Matrix Summary view in OKR reports.

Variant types returned are SNV/INDEL, CNV, fusions, and RNAExonVariants.