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allow_indels
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Candidate generation parameter: Allow INDEL candidates to be generated when set.
Allowed values: 0 = does not generate indel candidates, 1 = generates INDEL candidates
Suggested trial value: 1
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allow_snps
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Candidate generation parameter: Allow SNP candidates to be generated when set.
Allowed values: 0 = does not generate SNP candidates, 1 = generates SNP candidates
Suggested trial value: 1
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allow_mnps
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Candidate generation parameter: Allow MNP candidates to be generated when set.
Allowed values: 0 = does not generate MNP candidates , 1 = generates MNP candidates
Suggested trial value: 1
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allow_complex
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Candidate generation parameter: Allow complex variant candidates to be generated when set.
Allowed values: 0 = does not generate complex candidates, 1 = generates complex candidates
Suggested trial value: 1
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gen_min_alt_allele_freq
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A candidate generation parameter: A non-HP-INDEL candidate needs to have an allele frequency greater than this value in the pileup.
Allowed values:Decimal numbers between 0 and 1
Suggested trial value: 0.02 to 0.15
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gen_min_indel_alt_allele_freq
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A candidate generation parameter: An HP-INDEL candidate needs to have an allele frequency greater than this value in the pileup.
Allowed values: Decimal numbers between 0 and 1
Suggested trial value: 0.02 to 0.15
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gen_min_coverage
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A candidate generation parameter: A variant candidate location needs to have coverage depth greater than this value.
Allowed values: Integers ≥ 0
Suggested trial value: 6
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min_mapping_qv
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A read filtering parameter: Minimum mapping quality value required for a read to be counted (for both candidate generation and variant evaluation).
Allowed values: ≥ 0
Suggested trial value: 4
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read_snp_limit
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A read filtering parameter: Do not use reads with number of SNPs above this.
Allowed values: Integers ≥ 0
Suggested trial value: 10
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read_max_mismatch_fraction
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A read filtering parameter: Ignore reads with fraction of mismatch greater than this value.
Allowed values: Decimal numbers between 0 and 1
Suggested trial value: 1.0
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min_cov_fraction
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A read filtering parameter: Do not use reads with fraction of covering the best assigned unmerged target region below this.
Allowed values: Decimal numbers between 0 and 1
Suggested trial value: 0.9 (TagSequending and Ion AmpliSeq™ HD), 0 (otherwise)
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read_mismatch_limit
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A read filtering parameter: Do not use reads with number of mismatches (where 1 gap open counts 1) above this value.
Allowed values: Integers ≥ 0 (0 disables the filter)
Suggested trial value: 5 (Tag Sequencing and Ion AmpliSeq™ HD), 0 (other)
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