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 |
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Filter: Phred-scaled minimum average evidence per read or no-call. Related VCF field: MLLD. |
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Reduce coverage in over-sampled locations to this value. |
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Filter: Minimum coverage required on each strand. |
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Filter: Phred-scaled evidence that the reads support a variant above minimum frequency. |
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Frequency cutoff for supporting a variant. |
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Total coverage required of reads or no-call. |
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Filter: proportion of variant alleles comes overwhelmingly from one strand. Related VCF field: STB. |
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Filter: Minimum coverage required on each strand. |
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Filter: Phred-scaled evidence that the reads support a variant above minimum frequency. |
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Frequency cutoff for supporting a variant. |
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Total coverage required of reads or no-call. |
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Filter: proportion of variant alleles comes overwhelmingly from one strand. Related VCF field: STB. |
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Filter: Minimum coverage required on each strand. |
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Phred-scaled evidence that the reads support a variant above minimum frequency. |
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Frequency cutoff for supporting a variant. |
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Total coverage required of reads or no-call. |
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Filter: proportion of variant alleles comes overwhelmingly from one strand. Related VCF field: STB. |
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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. |
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Number of pseudo-data-points suggesting our predictions match the measurements without bias. |
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Prior probability that a read comes from some other distribution. |
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How heavy the t-distribution tails are to allow for unusual spread in the data. |
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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)]. |
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Filter: observed clusters deviate from predictions more than this amount (relative to the size of the variant). Related VCF fields: VARB, REFB. |
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Filter: observed clusters deviate from predictions more than this amount (relative to the size of the variant). Related VCF fields: VARB, REFB. |
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Filter: homopolymer length involved in an in/del. Related VCF field: HRUN. |
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Realign reads in the vicinity of SNP candidates. Impact: True = do not realign, False = realign. |
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Recalibration values from pipeline used or not (experimental). No related fields, changes basecalling behavior. Allowed values: True = allow recalibration, False = don't allow recalibration. |
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Filter out variants in motifs with error rates above this. |
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Filter: Minimum coverage required on each strand. |
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Filter out MNPs with a QUAL score less than or equal to this Phred-scaled value. |
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Frequency cutoff for supporting a variant. |
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Total coverage required of reads or no-call. |
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Filter: proportion of variant alleles comes overwhelmingly from one strand. Related VCF field: STB. |
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Filter out mnps with pval below this [1.0] given strand bias > mnp-strand-bias. |
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Filter out snps with pval below this [1.0] given strand bias > snp-strand-bias. |
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Filter out INDELs with pval below this [1.0] given strand bias > INDEL-strand-bias. |
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Filter out hotspot variants with pval below this [1.0] given strand bias > hotspot-strand-bias. |
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Skip position bias filter if (reference read count)/(reference + alt allele read count) less than or equal to this. |
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Filter out variants with position bias relative to soft clip ends in reads > position-bias. |
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Filter out if position bias is above the Position Bias given pval less than Position Bias Pvalue. |
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Enable the position bias filter. |
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Apply INDEL filters to non HP INDELs. |
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Realign reads in the vicinity of candidate mnp variants. |
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Maximum allowed fraction of reads where realignment causes an alignment change. |
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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. |
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Do not use reads with number of mismatches (where 1 gap open counts 1) above this value. |
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Do not count reads with fraction of covering any amplicons below this threshold. |
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Only consider provided alleles in the hotspots file. 0 = generate de novo candidates, 1 = hotspots only. |
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Sets defaults for counting reads in liquid biopsy runs with ampliseq-hd using "tvc consensus". |
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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. |
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Minimum mapping quality value required for a read to be counted. |
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Use Poisson parameter estimation to estimate count of functional families. |
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Minimum number of variant supporting functional families required to make a SNP call. Impact: Increasing values make variant calls less sensitive but more specific. |
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Minimum number of variant supporting functional families required to make a MNP call. Impact: Increasing values make variant calls less sensitive but more specific. |
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Minimum number of variant supporting functional families required to make a INDEL call. Impact: Increasing values make variant calls less sensitive but more specific. |
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Minimum number of variant supporting functional families required to make a hotspot call. Impact: Increasing values make variant calls less sensitive but more specific. |
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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. |
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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. |
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Minimum required coverage of reads on each strand in a bi-directional molecular tag family. |
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Minimum callable probability for LOD calculation. |
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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. |
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Enable INDELs in FreeBayes hypothesis generator. Allowed values: True = generate INDEL hypotheses, False = don't generate. |
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Enable SNPs in FreeBayes hypothesis generator. Allowed values: True = generate SNP hypotheses, False = don't generate. |
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Enable MNPs in FreeBayes hypothesis generator. Allowed values: True = generate MNP hypotheses, False = don't generate. |
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Enable complex variants in FreeBayes hypothesis generator. Allowed values: True = generate MNP hypotheses, False = don't generate. |
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Minimum mapping QV value required for reads to be allowed into the pileup (both FreeBayes and evaluator). |
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Read mismatch limit on number of mismatches: filter potential mis-mapped reads. |
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Read maximum mismatch fraction of mismatches in length of read: filter potential mis-mapped reads. |
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Generate variants with at least this frequency in the pileup. |
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Generate INDEL variants with at least this frequency in the pileup. |
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Generate variants in locations with at least this depth of coverage. |
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Size of the smallest k-mer used in assembly. Impact: Increasing values make INDEL calls less sensitive but more specific. |
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Minimum support for a variant to be evaluated. Impact: Increasing values make INDEL calls less sensitive but more specific. |
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Minimum assembled sequence match on both sides of the variant. Impact: Increasing values make INDEL calls less sensitive but more specific. |
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Minimum size INDEL reported by assembly. Impact: Increasing values make INDEL calls less sensitive but more specific. |
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Variants containing HP larger than this are not reported. Impact: Increasing values make INDEL calls more sensitive but less specific. |
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Minimum frequency of the variant to be reported. Impact: Increasing values make INDEL calls less sensitive but more specific. |
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Variants with strand bias above this are not reported. Impact: Increasing values make INDEL calls more sensitive but less specific. |
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Enables reporting of complex variants. Impact: 1 = report complex variants, 0 = don't report. |
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Represent variants with Locus view or Allele view. For more information, see Locus View versus Allele View of variants. |
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Analysis strand specific error file. Select a mask from the list or upload a mask from Upload. |
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