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X_min_allele_freq
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X is one of the allele types in {indel, snp, mnp, hotspot}.
A variant evaluation parameter: The presence of the allele of the type is defined by which allele frequency is greater than this value.
Allowed values: Decimal between 0 and 1
Suggested trial value: between 0.01 (somatic) and 0.2 (germline)
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X_min_variant_score
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X is one of the allele types in {indel, snp, mnp, hotspot}.
A filter parameter: A called allele of the type needs to have a QUAL score greater than this Phred-scaled value.
Filter reason: quality score.
Related VCF fields: QUAL
Allowed values: Decimal values ≥ 0
Suggested trial value: > 10
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X_min_coverage
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X is one of the allele types in {indel, snp, mnp, hotspot}.
A filter parameter: The location of a called allele of the type needs to have a coverage greater than this value.
Filter reason: MINCOV
Related VCF fields: FRO, FAO
Allowed values: Integers ≥ 0
Suggested trial value: between 5 and 20
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X_min_cov_each_strand
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X is one of the allele types in {indel, snp, mnp, hotspot}.
A filter parameter: Minimum coverage required on each strand for a the type of allele to be called.
Filter reason: PosCov or NegCov
Related VCF fields: FSRF, FSRR, FSAF, FSAR
Allowed values: Integers ≥ 0
Suggested trial value: ≥ 3
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X_strand_bias
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X is one of the allele types in {indel, snp, mnp, hotspot}.
A filter parameter: A candidate allele of the type will be filtered out if its strand bias p-value is less than
X_strand_bias_pval, and its strand bias is greater than
X_strand_bias. The parameter is critical for filtering out the false positive calls due to the strand-specific sequencing error.
Filter reason: STDBIAS and STDBIASPVAL
Related VCF field: STB
Allowed values: Decimal numbers between 0.5 (requires perfect balance on both strands) and 1.0 (tolerates extremely strong strand bias)
Suggested trial value: 0.95
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X_strand_bias_pval
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X is one of the allele types in {indel, snp, mnp, hotspot}.
A filter parameter: A candidate allele of the type will be filtered out if its strand bias p-value is less than
X_strand_bias_pvall and its strand bias is greater than
X_strand_bias.
Filter reason: STDBIAS and STDBIASPVAL
Related VCF field: STBP
Allowed values: Decimal numbers between 0 and 1
Suggested trial value: 0.01 for strand bias filter, 1 for no strand bias filter
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X_min_var_coverage
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X is one of the allele types in {indel, snp, mnp, and hotspot}.
A filter parameter: Minimum number of variant coverage after flow-evaluation required to make the call.
Filter reason: VarCov
Related VCF field: FAO
Allowed values: Integer ≥ 0
Suggested trial value: 3 (TagSequencing or AmpliSeq HD), 0 (other)
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downsample_to_coverage
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Reduce coverage in over-sampled locations to this value to save computational time.
Allowed values: Integers ≥1
Suggested trial value: 400 (germline), 2000 (somatic)
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use_fd_param
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(experimental in Torrent Suite™ Software 5.4)
A filtering parameter: Use Flow Disruptiveness (FD) instead of allele types (INDEL, SNP, MNP) as the criterion to select the parameter set.
If turned on, the (non-FD, weak FD, strong FD) allele applies the (INDEL, SNP, MNP) parameters, respectively.
If powered on, the (non-FD, weak FD, strong FD) allele applies the (INDEL, SNP, MNP) parameters, respectively.
Allowed values: 0: do not use FD parameters, 1: use FD parameters.
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data_quality_stringency
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A filter parameter: A called variant needs to have a mean log-likelihood difference per read greater than this Phred-scaled value.
Filter reason: STRINGENCY
Related VCF field: MLLD
Allowed values: Decimal numbers ≥ 0
Suggested trial value: ≥ 6.5
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filter_unusual_predictions
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A filter parameter: A called variant needs to have RBI less than this value. The parameter is critical for filtering out the false positive calls due to the strand-specific sequencing error.
Filter reason: PREDICTIONSHIFTx
Related VCF fields: RBI = sqrt(FWDB ^ 2 + REVB ^ 2)
Allowed values: Decimal numbers ≥ 0
Suggested trial value: 0.3
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filter_deletion_predictions
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A filter parameter: Filter out a deletion if the observed clusters deviate from predictions more than this amount.
Filter reason: PREDICTIONVarSHIFTx or PREDICTIONRefSHIFTx
Related VCF fields: VARB, REFB
Allowed values: Decimal numbers ≥ 0
Suggested trial value: 0.2
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filter_insertion_predictions
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A filter parameter: Filter out an insertion if the observed clusters deviate from predictions more than this amount.
Filter reason: PREDICTIONVarSHIFTx or PREDICTIONRefSHIFTx
Related VCF fields: VARB, REFB
Allowed values: Decimal numbers ≥ 0
Suggested trial value: 0.2
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min_callable_prob
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A reporting parameter (TagSeq/AmpliSeq HD only): The minimum callable probability for the calculation of Limit Of Detection (LOD).
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min_fam_per_strand_cov
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An evaluation parameter for Tag Sequencing and Ion AmpliSeq™ HD runs only: Minimum required coverage of reads on each strand in a bi-directional functional molecular tag family.
Allowed values: Integers ≥ 0
Suggested trial value: 1
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min_tag_fam_size
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An evaluation parameter for Tag Sequencing and Ion AmpliSeq™ HD runs only: Minimum number of reads with same molecular tag required to form a functional molecular family.
Allowed values: Integer ≥ 1
Suggested trial value: 3
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tag_trim_method
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An evaluation parameter for Tag Sequencing and Ion AmpliSeq™ HD only: Requirement of the molecular tag of the read must match the format specified in the Planned Run.
Allowed values: strict-trim (requires match), sloppy-trim (does not require match)
Suggested trial value: sloppy-trim
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indel_func_size_offset
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An evaluation parameter for Tag Sequencing and Ion AmpliSeq™ HD runs only: requires a family size ≥ (min_tag_fam_size + this value) to be functional for calling HP-INDEL.
Allowed values: Integers ≥ 0
Suggested trial value: 0
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heavy_tailed
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A variant evaluation parameter: (2*heavy_tailed-1) is the degree of freedom of the t-distribution for modeling the heavy tail in signal residual distribution.
Allowed values: Integers ≥ 1
Suggested trial value: 3
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outlier_probability
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A variant evaluation parameter: probability that a read comes from none of the models under consideration.
The variantCaller plugin will make NOCALL with filter reason REJECTION if FXX is too high.
Related VCF field: FXX
Allowed values: Decimal numbers between 0 and 1.0
Suggested trial value: between 0.005 and 0.01
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prediction_precision
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A variant evaluation parameter: The number of pseudo data points suggesting our predictions match the measurements without bias.
Allowed values: Decimal numbers ≥ 0.1
Suggested trial value: 1.0
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max_flows_to_test
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A variant candidate evaluating parameter: The maximum number of scoring flows being used.
Allowed values: Integers > 0
Suggested trial value: 10
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suppress_recalibration
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A variant evaluation parameter: Homopolymer recalibration values should not be used when set.
Allowed values: 0 = enable recalibration, 1 = disable recalibration
Suggested trial value: 0
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do_snp_realignment
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A variant candidate evaluating parameter: Realign reads in the vicinity of SNP candidates when set.
Related VCF content: REALIGNEDx
Allowed values: 0 = do not realign, 1 = realign
Suggested trial value: 0
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do_mnp_realignment
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A variant candidate evaluating parameter: Realign reads in the vicinity of MNP candidates when set.
Related VCF content: REALIGNEDx
Allowed values: 0 = do not realign, 1 = realign
Suggested trial value: 0
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realignment_threshold
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A variant candidate evaluating parameter: Maximum allowed fraction of reads where realignment causes an alignment change.
Related VCF content: SKIPREALIGNx
Allowed values: Decimals between 0 and 1
Suggested trial value: 1
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min_ratio_for_fd
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A filter parameter: Claim flow-disruption if the portion of reads that are flow-disrupted greater than or equal to this value.
Allowed values: Decimal numbers between 0 and 1
Suggested trial value: 0.1
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indel_as_hpindel
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A filter parameter: A flag indicating whether INDEL filters or SNP filters should be applied to non-HP INDELs.
Allowed values: 0 (false), 1 (true)
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hp_max_length
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A filter parameter: HP indels of more than this length will be filtered out.
Filter reason: HPLEN
Related VCF field: HRUN
Allowed values: Integers ≥ 1
Suggested trial value: 8
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hp_indel_hrun
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A filter parameter: Define the HRUN for filtering HP-INDEL variants with lengths specified by
hp_del_len and
hp_ins_len.
Filter reason: HPINSLEN, HPDELLEN
Related VCF field: HRUN
Allowed values: Vector of positive integers (for example, [1,2,3]) with size matches
hp_del_len and
hp_ins_len
Suggested trial value: []
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hp_ins_len
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A filter parameter: Filter out HP-INS variants whose INS length is less than or equal to the corresponding entry of this vector if the HRUN is defined in
hp_indel_hrun.
Filter reason: HPINSLEN
Related VCF field: HRUN
Allowed values: Vector of non-negative integers (for example, [1,2,3]) with size matches
hp_del_len and
hp_indel_hrun.
Suggested trial value: []
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hp_del_len
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A filter parameter: Filter out HP-DEL variants whose DEL length is less than or equal to the corresponding entry of this vector if the HRUN is defined in 'hp_indel_hrun'.
Filter reason: HPDELLEN
Related VCF field: HRUN
Allowed values: Vector of nonnegative integers (for example, [1,2,3]) with size matches
hp_ins_len and
hp_indel_hrun.
Suggested trial value: []
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use_position_bias
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A filter parameter: Enable the position bias filter when set.
Filter reason: POSBIAS, POSBIASPVAL
Allowed values: 0 = disable, 1= enable
Suggested trial value: (AmpliSeq) 1, (other) 0
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position_bias
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A filter parameter: Filter out a variant if the position bias is greater than
position_bias and the position bias p-value is less than
position_bias_pval.
Filter reason: POSBIAS, POSBIASPVAL Related VCF field: POSBIAS
Allowed values: Ddecimal numbers between 0 and 1
Suggested trial value: 0.75
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position_bias_pval
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A filter parameter: Filter out a variant if the position bias is greater than
position_bias and the position bias p-value is less than
position_bias_pval.
Filter reason: POSBIAS, POSBIASPVAL Related VCF field: POSBIASPVAL
Allowed values: Decimal numbers between 0 and 1
Suggested trial value: 0.05
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position_bias_ref_fraction
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A filter parameter: Skip the position bias filter if (reference read count) / (reference and alt read count) ≤ this value.
Filter reason: POSBIAS, POSBIAS-PVAL
Allowed values: Decimal numbers between 0 and 1
Suggested trial value: 0.05
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error_motifs
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The file name of the error motif file
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sse_prob_threshold
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A filter parameter: Filter threshold for motif-predicted error probability.
Filter reason: NOCALLxPredictedSSE, NOCALLxPositiveSSE, NOCALLxNegativeSSE
Related VCF fields: SSEP, SSEN
Allowed values: Decimal numbers between 0 and 1
Suggested trial value: 0.02
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report_ppa
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A reporting parameter: Report Possible Polyploidy Alleles (PPA) in the VCF file and the variant calls in the XLS files.
Related VCF field: PPA
Allowed values: 1 = report PPA, 0 = do not report
Note: This feature is experimental and by default is set to
report_ppa = 0 (do not report).
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