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 user-defined filter chains that are built from predefined filter chains, or from one or more filters. For more information, see Create a user-defined filter chain.

The available filter chain version depends on the versions of the analysis workflows that are installed in the software. It is recommended that you use the filter chain version that is compatible with the analysis workflow that you use. Some predefined filter chains are selected by default as the compatible filter chain when you create or edit an analysis workflow, or view analysis results.

Details, including the version and the logic that is used by each filter chain, can be viewed in the software. For more information, see View filter chain details.


Predefined filter chain name	Available versions	Reference genome	Description
AmpliSeq Exome Tumor Normal v1	5.16 5.18 5.20 5.22	hg19	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	5.16 5.18 5.20 5.22	hg19	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	5.16 5.18 5.20 5.22	hg19	This filter chain reports all hotspot variants that pass the filter and are not called as reference or NOCALL. Variant types include SNV, INDEL, MNV, and RNA Exon Tiles.
Called Variants and Controls	5.16 5.18 5.20 5.22	hg19	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 FLT3-ITD, RNA Exon Tiles.
CNVs of Confidence ≥0.1–Germline–CNVs only	5.16 5.18 5.20 5.22	hg19	For germline analyses, this filter chain narrows the analysis results to copy number variants with a confidence value of ≥0.1.
Confident Germline CNVs–CNVs Only	5.16 5.18 5.20 5.22	hg19	For germline analyses, this filter chain narrows the analysis results to copy number variants with a confidence value of ≥10. Not a default filter.
Confident Somatic CNVs–CNVs Only	5.16 5.18 5.20 5.22	hg19	This filter chain includes 5% confidence interval range and 95% confidence interval range.
Default CarrierSeq View	5.16	GRCh38	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™ Ion CarrierSeq™ ECS Kits User Guide, MAN0018483.
Default DNA and Fusions View	5.16 5.18 5.20 5.22	hg19	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	5.16 5.18 5.20 5.22	hg19	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 Germline Variants view	5.22	hg19	This is the default filter chain of the Ion AmpliSeq™ germline custom CNV workflow or assay to refine their copy number variation (CNV) analysis results. It returns CNVs based on the specific filter conditions and all “Present” SNV/INDEL and fusion variants. To pass this filter, CNVs must meet specific confidence thresholds. You can enable or disable the default filter chain during assay creation and in the CNV results table.
Default Germline Variants view GRCh38	5.22	GRCh38	This is the default filter chain of the Ion AmpliSeq™ germline custom CNV workflow or assay to refine their copy number variation (CNV) analysis results. It returns CNVs based on the specific filter conditions and all “Present” SNV/INDEL and fusion variants. To pass this filter, CNVs must meet specific confidence thresholds. You can enable or disable the default filter chain during assay creation and in the CNV results table.
Default Somatic Variants view	5.22	hg19	This is the default filter chain of the Ion AmpliSeq™ somatic custom CNV workflow or assay to refine copy number variation (CNV) analysis results. This filter chain defines criteria for both copy number amplification (gain) and depletion (loss). Only targets that meet these criteria are reported in the results table when the filter chain is applied. You can enable or disable the default filter chain during assay creation and in the CNV results table.
Default Somatic Variants view GRCh38	5.22	GRCh38	This is the default filter chain of the Ion AmpliSeq™ somatic custom CNV workflow or assay to refine copy number variation (CNV) analysis results. This filter chain defines criteria for both copy number amplification (gain) and depletion (loss). Only targets that meet these criteria are reported in the results table when the filter chain is applied. You can enable or disable the default filter chain during assay creation and in the CNV results table.
Default Variant View	5.16 5.18 5.20 5.22	hg19	This filter chain narrows the analysis results to confident variant types, which are not CNVs, but can include SNV, INDEL, MNV, REF, NOCALL, LONGDEL, FUSION, EXPR_CONTROL, ASSAYS_5P_3P, RNA_HOTSPOT, GENE_EXPRESSION, RNAExonVariant, ProcControl, and FLT3-ITD.
Genetic Disease Variants	5.16 5.18 5.20 5.22	hg19	This filter chain narrows the 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.
Oncomine™ BRCA	5.16 5.18 5.20 5.22	hg19	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	5.22 5.18 5.20	hg19	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: Targeted and non-targeted fusions. CNV variants with FILTER value of GAIN or LOSS. Likely somatic mutations based on dbSNP, 5000Exomes, gnomAD (ExAC in versions 5.18 and 5.20), 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.
Oncomine Extended GRCh38	5.22	GRCh38	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: Targeted and non-targeted fusions. CNV variants with FILTER value of GAIN or LOSS. Likely somatic mutations based on dbSNP, 5000Exomes, gnomAD (ExAC in versions 5.18 and 5.20), 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.
Oncomine™ Variants	5.18 5.20 5.22	hg19	This filter chain includes all Oncomine™-annotated variants.
Oncomine™ Variants, 5% CI CNV ploidy ≥gain of 2 over normal	5.20 5.22	hg19	This filter chain restricts copy number variants to gains of >2 based on the 5% confidence interval level. It also returns Oncomine™-annotated variants.
TMB (Non-germline Mutations)	5.18 5.20 5.22	hg19, GRCh38	This filter chain returns results for somatic variants based on dbSNP, 5000Exomes, gnomAD (ExAC in versions 5.18 and 5.20), 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 >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 by the use of this filter chain cannot be changed after an analysis is complete. The filter chain is applied before the parameter application. The filtered variant file is passed to the TML script that further applies the user parameters.
TMB GRCh38 (Non-germline Mutations)	5.18 5.20 5.22	GRCh38	This filter chain returns results for somatic variants based on dbSNP, 5000Exomes, gnomAD (ExAC in versions 5.18 and 5.20), 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 >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 by the use of this filter chain cannot be changed after an analysis is complete. The filter chain is applied before the parameter application. The filtered variant file is passed to the TML script that further applies the user parameters.
Variant Matrix Summary	5.16 5.18 5.20 5.22	hg19	Select this filter chain for analysis results that include the same set of variants that are included in the Variant Matrix Analysis visualization for Ion AmpliSeq™ HD analysis results. The Variant Matrix Summary filter chain filters in: Positive hotspot calls Positive gene-level CNV, GAIN, or LOSS calls FLT3-ITD variants Non-wild-type intragenic structural variations For TagSeq Breast and TagSeq Pan-Cancer assays: non-hotspot variants in TP53 with QUAL >50 and Allele Frequency > 1.0 (Breast) or 0.5 (Pan Cancer) This filter chain allows analysis results to be exported. You can then import the results into another software application for further analysis. Filter variant types include: SNV/INDEL, CNV, fusions, and RNAExonVariants. If you use the Oncomine™ Myeloid MRD analysis workflow, a FLT3-ITD variant subtype named Combined can be reported in analysis results. The Combined subtype is a value for the sum of all reported FLT3-ITD variant allele frequencies.