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kmer_len
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Size of the smallest k-mer used in assembly.
Impact: Increasing values make INDEL calls less sensitive but more specific.
Allowed values: Integers ≥ 5
Suggested trial value: 11 and 30
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min_var_freq
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Minimum frequency of the variant to be reported.
Impact: Increasing values make INDEL calls less sensitive but more specific.
Allowed values: Decimal numbers between 0 and 1
Suggested trial value: 0.1 and 0.4
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min_var_count
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Minimum support for a variant to be evaluated.
Impact: Increasing values make INDEL calls less sensitive but more specific.
Allowed values: Integers > 1
Suggested trial value: 3 and 30
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short_suffix_match
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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.
Allowed values: Integers > 2
Suggested trial value: 4 and kmer_len
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min_indel_size
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Minimum size indel reported by assembly.
Impact: Increasing values make INDEL calls less sensitive but more specific.
Allowed values: Integers > 0
Suggested trial value: 2 and 30
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max_hp_length
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Variants containing HP larger than this are not reported.
Impact: Increasing values make INDEL calls more sensitive but less specific.
Allowed values: Integers > 1
Suggested trial value: 2 and 11
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relative_strand_bias
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Variants with strand bias above this are not reported.
Impact: Increasing values make INDEL calls more sensitive but less specific.
Allowed values: Decimal numbers between 0 and 1
Suggested trial value: 0.6 and 1.0
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output_mnv
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Enables reporting of complex variants.
Allowed values: 1 = report complex variants, 0 = don't report
Suggested trial value: 0
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