downsample_to_coverage

Reduce coverage in over-sampled locations to this value to save computational time

Allowed values: Integers >= 1

Suggested trial value 400 (germline), 2000 (somatic)

heavy_tailed

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

outlier_probability

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

prediction_precision

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

min_detail_level_for_fast_scan

A variant candidate evaluating parameter: The minimum detail-level to trigger the fast scan algorithm that considerably speeds up the evaluator.

Allowed values: >=0 (0 = always apply the fast scan algorithm)

Suggested trial value: 0

max_flows_to_test

A variant candidate evaluating parameter: The maximum number of scoring flows being used.

Allowed values: Integers > 0

Suggested trial value 10 (20 if the Hotspots file contains long variants)

suppress_recalibration

A variant evaluation parameter: Homopolymer recalibration values should not be used when set

Allowed values: 0 = allow recalibration, 1 = don't allow recalibration

Suggested trial value 0

do_snp_realignment

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

do_mnp_realignment

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

realignment_threshold

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

use_fd_param

(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 choose the parameter set.

If turned on, the (non-FD, moderate FD, FD) allele applies the the (INDEL, SNP, MNP) parameters, respectively.

Allowed values: 0: do not use FD parameters, 1: use FD parameters.

min_ratio_for_fd

A filter parameter: Claim flow-disruption if the portion of reads that are flow-disrupted >= this value

Allowed values: Decimal numbers between 0 and 1

Suggested trial value 0.1

indel_as_hpindel

A filter parameter: A flag indicating whether INDEL filters or SNP filters should be applied to non-HP indels

Allowed values: 0 = use SNP filter, 1 = use INDEL filter

Suggested trial value (AmpliSeq) 1, (other) 0

X_min_allele_freq

X is one of the allele type 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 and 0.2

X_min_variant_score

X is one of the allele type 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 Related VCF fields: QUALFilter reason: QualityScore Allowed values: Integers >= 0 Suggested trial value >= 10

X_min_coverage

X is one of the allele type 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

X_min_cov_each_strand

X is one of the allele type 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

X_strand_bias

X is one of the allele type 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

Filter reason: STDBIAS and STDBIASPVAL

Related VCF field: STB

Allowed values: Decimal numbers between 0.5 and 1.0

Suggested trial value 0.95

X_strand_bias_pval

X is one of the allele type 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_snp_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

data_quality_stringency

A filter parameter: A called variant needs to have a mean log-likelihood difference per read greater than this Phred-scaled value

Related VCF field: MLLD Filter reason: STRINGENCYAllowed values:

Decimal numbers >= 0

Suggested trial value >= 6.5

filter_unusual_predictions

A filter parameter: A called variant needs to have RBI less than this value

Filter reason: PREDICTIONSHIFTx Related VCF fields: RBI = sqrt(FWDB ^ 2 + REVB ^ 2)

Allowed values: Decimal numbers >= 0

Suggested trial value 0.3

filter_deletion_predictions

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

filter_insertion_predictions

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

hp_max_length

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

hp_indel_hrun

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 (e.g. [1,2,3]) with size matches 'hp_del_len' and 'hp_ins_len'.

Suggested trial value []

hp_ins_len

A filter parameter: Filter out HP-INS variants whose INS length <= 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 (e.g. [1,2,3]) with size matches 'hp_del_len' and 'hp_indel_hrun'.

Suggested trial value []

hp_del_len

A filter parameter: Filter out HP-DEL variants whose DEL length <= 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 non-negative integers (e.g. [1,2,3]) with size matches 'hp_ins_len' and 'hp_indel_hrun'.

Suggested trial value []

use_position_bias

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

position_bias

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: Decimal numbers between 0 and 1

Suggested trial value 0.75

position_bias_pval

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

position_bias_ref_fraction

A filter parameter: Skip the position bias filter if (reference read count) / (reference and alt read count) <= this value

Filter reason: POSBIAS, POSBIASPVAL

Allowed values: Decimal numbers between 0 and 1

Suggested trial value 0.05

error_motifs

The file name of the error motif file

sse_prob_threshold

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 0.2

report_ppa

(Torrent Suite Software 5.4) Report Possible Polyploidy Alleles (PPA) in the INFO FIELD of the vcf lines.

Related VCF field: PPA

Allowed values: 1 = report PPA, 0 = do not report