quality-based_variant_detection

--create-table <Boolean> Create table with annotated variants (default: false)
--create-track <Boolean> Create a track of variants, useful for further analysis (default: true)
-d, --destination <ClcUrl> Destination file or folder on server. If not specified the folder of the first input object will be used.
--enable-advanced <Boolean> Enable advanced significance settings: maximum coverage, and sufficient and required supporting read count thresholds. (default: false)
--genetic-code <Genetic code> Genetic code used for annotating variants with amino acid changes (default: 1 Standard)
-i, --input <ClcUrl> Input data on server
--ignore-broken-pairs <Boolean> (default: true)
--ignore-nonspecific-matches <Boolean> (default: true)
--iontorrent-454-correction <Boolean> Indels found in homopolymer regions are ignored. (default: false)
--log <Boolean> Enable creation of algo log file. (default: true)
--max-coverage
Integer: >= 1 Variants covered by more than this number of reads will not be called. (default: 99999)
--max-gaps-and-mismatches
Integer: >= 0 Any read where the neighborhood of a candidate variant contains more than this number of gaps and mismatches is considered of low quality and ignored for that variant. Must be at most twice the neighborhood radius. (default: 2)
--min-central-quality
Byte: 0 <= x <= 64 Applies only to reads that have quality scores. Any read where the bases included in a candidate variant have average quality score less than this number is considered of low quality and ignored for that variant. (default: 20)
--min-coverage
Integer: >= 1 Variants covered by less than this number of reads will not be called. (default: 10)
--min-neighborhood-quality
Byte: 0 <= x <= 64 Applies only to reads that have quality scores. Any read where the bases in the neighborhood of a candidate variant have average quality less than this number is considered of low quality and ignored for that variant. (default: 15)
--min-read-freq
Double: 0.0 < x <= 100.0 Variants with a frequency less than this number will not be called. (default: 35.0)
--neighborhood-radius
Integer: >= 0 The radius of the neighborhood considered for each read to assess read quality around a candidate variant position. The number of read residues considered will be twice the neighborhood radius. (default: 5)
--ploidy
Integer: >= 1 The maximum number of alleles expected for each variant. This should be equal to the ploidy of the sequenced genome, eg. 2 for a diploid organism. (default: 2)
--required-read-count
Integer: >= 1 Variants whose supporting read count is less than this number will not be called. (default: 1)
--sufficient-read-count
Integer: >= 1 Variants whose supporting read count is at least this number will be called irrespective of the minimum frequency setting. (default: 5)
--variant-in-forward-reverse-reads
<Boolean> Variants should be supported by at least 5