Variant Finding parameters
You can adjust the following Variant Finding parameters to optimize your analysis results when you create or edit analysis workflows.
IMPORTANT! Use the default parameter settings unless you are an advanced user.
Parameter Name | Description |
|---|---|
Main tab | |
Analysis | |
Data Quality Stringency | Filter: Phred-scaled minimum average evidence per read or no-call. Related VCF field: MLLD. Allowed values: 0 to unlimited |
Downsample to Coverage | Reduce coverage in over-sampled locations to this value. Allowed values: 1 to unlimited |
SNP Min Cov Each Strand | Filter: Minimum coverage required on each strand. Allowed values: 0 to unlimited |
SNP Min Variant Score | Filter: Phred-scaled evidence that the reads support a variant above minimum frequency. Allowed values: 0 to unlimited |
SNP Min Allele Freq | Frequency cutoff for supporting a variant. Allowed values: 0 to 1.0 (decimals) |
SNP Min Coverage | Total coverage required of reads or no-call. Allowed values: 0 to unlimited |
SNP Strand Bias | Filter: proportion of variant alleles comes overwhelmingly from one strand. Related VCF field: STB. Allowed values: 0.5 to 1.0 (decimals) |
INDEL Min Cov Each Strand | Filter: Minimum coverage required on each strand. Allowed values: 0 to unlimited |
INDEL Min Variant Score | Filter: Phred-scaled evidence that the reads support a variant above minimum frequency. Allowed values: 0 to unlimited (integers) |
INDEL Min Allele Freq | Frequency cutoff for supporting a variant. Allowed values: 0 to 1.0 (decimals) |
INDEL Min Coverage | Total coverage required of reads or no-call. Allowed values: 0 to unlimited (integers) |
INDEL Strand Bias | Filter: proportion of variant alleles comes overwhelmingly from one strand. Related VCF field: STB. Allowed values: 0.5 to 1.0 (decimals) |
Hotspot Min Cov Each Strand | Filter: Minimum coverage required on each strand. Allowed values: 0 to unlimited (integers |
Hotspot Min Variant Score | Phred-scaled evidence that the reads support a variant above minimum frequency. Allowed values: 0 to unlimited (integers) |
Hotspot Min Allele Freq | Frequency cutoff for supporting a variant. Allowed values: 0 to 1.0 (decimals) |
Hotspot Min Coverage | Total coverage required of reads or no-call. Allowed values: 0 to unlimited (integers) |
Hotspot Strand Bias | Filter: proportion of variant alleles comes overwhelmingly from one strand. Related VCF field: STB. Allowed values: 0.5 to 1.0 (decimals) |
PPA | Reports Possible Polyploidy Alleles (PPA) in the INFO FIELD of the VCF file. Related VCF field: PPA. Allowed values: 1 = report PPA, 0 = do not report. 1 is recommended for somatic-only and experimental research. If PPA is set to True and Variant View advanced parameter is set to Allele View, a PPA column is included in the Analysis Results screen. A value of Yes indicates variants that are PPA alleles. No indicates variants that are not PPA alleles. PPA must be set to True for the Possible Polyploidy Alleles filter to function. For more information, see Locus View versus Allele View of variants. Allowed values: True or False |
Prediction Precision | Number of pseudo-data-points suggesting our predictions match the measurements without bias. Allowed values: 0 to unlimited (decimals) |
Outlier Probability | Prior probability that a read comes from some other distribution. Allowed values: 0 to 1 (decimals) |
Heavy Tailed | How heavy the t-distribution tails are to allow for unusual spread in the data. Allowed values: 0 to unlimited (decimals) |
Filter Unusual Predictions | Filter: predictions are distorted to fit the data more than this distance (relative to the size of the variant). Related VCF fields: FWDB, REVB [RBI = sqrt(FWDB ^ 2 + REVB ^ 2)]. Allowed values: 0 to unlimited (decimals) |
Filter Insertion Predictions | Filter: observed clusters deviate from predictions more than this amount (relative to the size of the variant). Related VCF fields: VARB, REFB. Allowed values: 0 to unlimited (decimals) |
Filter Deletion Predictions | Filter: observed clusters deviate from predictions more than this amount (relative to the size of the variant). Related VCF fields: VARB, REFB. Allowed values: 0 to unlimited (decimals) |
HP Max Length | Filter: homopolymer length involved in an in/del. Related VCF field: HRUN. Allowed values: 1 to unlimited (integers) |
Do SNP Realignment | Realign reads in the vicinity of SNP candidates. Impact: True = do not realign, False = realign. Allowed values: True or False |
Suppress Recalibration | Recalibration values from pipeline used or not (experimental). No related fields, changes basecalling behavior. Allowed values: True = allow recalibration, False = don't allow recalibration. Allowed values: True or False |
SSE Probability Threshold | Filter out variants in motifs with error rates above this. Allowed values: 0 to 1 |
MNP Min Cov Each Strand | Filter: Minimum coverage required on each strand. Allowed values: 0 to unlimited (integers) |
MNP Min Variant Score | Filter out MNPs with a QUAL score less than or equal to this Phred-scaled value. Allowed values: 0 to unlimited |
MNP Min Allele Freq | Frequency cutoff for supporting a variant. Allowed values: 0 to 1 |
MNP Min Coverage | Total coverage required of reads or no-call. Allowed values: 0 to unlimited (integers) |
MNP Strand Bias | Filter: proportion of variant alleles comes overwhelmingly from one strand. Related VCF field: STB. Allowed values: 0.5 to 1 |
MNP Strand Bias Pval | Filter out mnps with pval below this [1.0] given strand bias > mnp-strand-bias. Allowed values: 0 to 1 |
SNP Strand Bias Pval | Filter out snps with pval below this [1.0] given strand bias > snp-strand-bias. Allowed values: 0 to 1 |
INDEL Strand Bias Pval | Filter out INDELs with pval below this [1.0] given strand bias > INDEL-strand-bias. Allowed values: 0 to 1 |
Hotspot Strand Bias Pval | Filter out hotspot variants with pval below this [1.0] given strand bias > hotspot-strand-bias. Allowed values: 0 to 1 |
Position Bias Reference Fraction | Skip position bias filter if (reference read count)/(reference + alt allele read count) less than or equal to this. Allowed values: 0 to 1 |
Position Bias | Filter out variants with position bias relative to soft clip ends in reads > position-bias. Allowed values: 0 to 1 |
Position Bias Pvalue | Filter out if position bias is above the Position Bias given pval less than Position Bias Pvalue. Allowed values: 0 to 1 |
Use position bias | Enable the position bias filter. Allowed values: True or False |
INDEL As HPINDEL | Apply INDEL filters to non HP INDELs. Allowed values: True or False |
Do MNP Realignment | Realign reads in the vicinity of candidate mnp variants. Allowed values: True or False |
Realignment Threshold | Maximum allowed fraction of reads where realignment causes an alignment change. Allowed values: 0 to 1 |
FD Nonsnp Min Var Cov | Override min_var_coverage of the flow-disrupted variants that are not SNPs (0 to disable the override). Impact: Decreasing values make variant calls less specific but more sensitive. Allowed values: 0 to 10 |
Read Mismatch Limit | Do not use reads with number of mismatches (where 1 gap open counts 1) above this value. Allowed values: 0 to unlimited |
Min Cov Fraction | Do not count reads with fraction of covering any amplicons below this threshold. Allowed values: 0 to 1 |
Use Input Allele Only | Only consider provided alleles in the hotspots file. 0 = generate de novo candidates, 1 = hotspots only. Allowed values: 0 to 1 |
Liquid Biopsy and Ion AmpliSeq™ HD | |
ampliseq-hd | Sets defaults for counting reads in liquid biopsy runs with ampliseq-hd using "tvc consensus". Allowed values: 0 to 1 |
Min Family Size | Minimum number of reads with same Unique Molecular Tag required to form a functional family. Impact: Increasing values make variant calls less sensitive but more specific. Allowed values: 0 to unlimited |
min-mapping-qv | Minimum mapping quality value required for a read to be counted. Allowed values: 0 to unlimited (integer) |
Poisson | Use Poisson parameter estimation to estimate count of functional families. Allowed values: 0 to 1 |
SNP Min Var Coverage | Minimum number of variant supporting functional families required to make a SNP call. Impact: Increasing values make variant calls less sensitive but more specific. Allowed values: 2 to 10 |
MNP Min Var Coverage | Minimum number of variant supporting functional families required to make a MNP call. Impact: Increasing values make variant calls less sensitive but more specific. Allowed values: 2 to 10 |
INDEL Min Var Coverage | Minimum number of variant supporting functional families required to make a INDEL call. Impact: Increasing values make variant calls less sensitive but more specific. Allowed values: 2 to 10 |
Hotspot Min Var Coverage | Minimum number of variant supporting functional families required to make a hotspot call. Impact: Increasing values make variant calls less sensitive but more specific. Allowed values: 2 to 10 |
INDEL Func Size Offset | Require family of size >= (min_tag_fam_size + this value) to be functional for calling HP-INDEL. Impact: Increasing values make variant calls less sensitive but more specific. Allowed values: 0 to 4 |
Tag Sim Max Cov | Check the similarity of UID of variant families if the variant molecular coverage is less than or equal to this value. Related VCF field: TGSM. Allowed values: 0 to unlimited |
Minimum Family Coverage per Strand | Minimum required coverage of reads on each strand in a bi-directional molecular tag family. Allowed values: 0 to unlimited |
Minimum Callable Probability | Minimum callable probability for LOD calculation. Allowed values: 0 to 1 |
Suppress called allele LOD | Suppress the LOD reporting of a variant allele that is called. This metric is useful to investigate possible false negatives. Do not use this metric as a filtering criteria. Allowed values: True or False |
Advanced tab | |
Analysis | |
Allow INDELs | Enable INDELs in FreeBayes hypothesis generator. Allowed values: True = generate INDEL hypotheses, False = don't generate. Allowed values: True or False |
Allow SNPs | Enable SNPs in FreeBayes hypothesis generator. Allowed values: True = generate SNP hypotheses, False = don't generate. Allowed values: True or False |
Allow MNPs | Enable MNPs in FreeBayes hypothesis generator. Allowed values: True = generate MNP hypotheses, False = don't generate. Allowed values: True or False |
Allow Complex | Enable complex variants in FreeBayes hypothesis generator. Allowed values: True = generate MNP hypotheses, False = don't generate. Allowed values: True or False |
Minimum mapping qv | Minimum mapping QV value required for reads to be allowed into the pileup (both FreeBayes and evaluator). Allowed values: 0 to unlimited (integer) |
Read SNP Limit | Read mismatch limit on number of mismatches: filter potential mis-mapped reads. Allowed values: 0 to unlimited (integer) |
Read Max Mismatch Fraction | Read maximum mismatch fraction of mismatches in length of read: filter potential mis-mapped reads. Allowed values: 0 to 1 (decimals) |
Generate Min Alt Allele Freq | Generate variants with at least this frequency in the pileup. Allowed values: 0 to 1 (decimals) |
Generate Min INDEL Alt Allele Freq | Generate INDEL variants with at least this frequency in the pileup. Allowed values: 0 to 1 (decimals) |
Generate Min Coverage | Generate variants in locations with at least this depth of coverage. Allowed values: 0 to unlimited |
Kmer Len | Size of the smallest k-mer used in assembly. Impact: Increasing values make INDEL calls less sensitive but more specific. Allowed values: 5 to unlimited (integers) |
Min Var Count | Minimum support for a variant to be evaluated. Impact: Increasing values make INDEL calls less sensitive but more specific. Allowed values: 1 to unlimited (integers) |
Short Suffix Match | Minimum assembled sequence match on both sides of the variant. Impact: Increasing values make INDEL calls less sensitive but more specific. Allowed values: 2 to unlimited (integers) |
Min INDEL Size | Minimum size INDEL reported by assembly. Impact: Increasing values make INDEL calls less sensitive but more specific. Allowed values: 1 to unlimited (integers) |
Max HP Length | Variants containing HP larger than this are not reported. Impact: Increasing values make INDEL calls more sensitive but less specific. Allowed values: 1 to unlimited (integers) |
Min Var Freq | Minimum frequency of the variant to be reported. Impact: Increasing values make INDEL calls less sensitive but more specific. Allowed values: 0 to 1 (decimals) |
Relative Strand Bias | Variants with strand bias above this are not reported. Impact: Increasing values make INDEL calls more sensitive but less specific. Allowed values: 0 to 1 (decimals) |
Output MNV | Enables reporting of complex variants. Impact: 1 = report complex variants, 0 = don't report. Allowed values: 0 to 1 (decimals) |
Variant View | Represent variants with Locus view or Allele view. For more information, see Locus View versus Allele View of variants. Allowed values: Locus view or Allele view |
Analysis SSE File | Analysis strand specific error file. Select a mask from the list or upload a mask from Upload. |