probabilistic_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 <ClcServerObjectUrl> Destination file or folder on server. If not specified the folder of the first input object will be used.
--discard-coalesced-snvs <Boolean> SNVs that have been coalesced into a longer variation will be discarded (default: true)
--genetic-code <Genetic code> Genetic code used for annotating variants with amino acid changes (default: 1 Standard)
-i, --input <ClcObjectUrl> Input data on server
--ignore-broken-pairs <Boolean> (default: true)
--ignore-nonspecific-matches <Boolean> (default: true)
--ignore-quality-scores <Boolean> (default: false)
--iontorrent-454-correction <Boolean> Indels found in homopolymer regions are ignored. (default: false)
--log <Boolean> Enable creation of algo log file. (default: true)
--min-coverage
Integer: >= 1 Variants covered by less than this number of reads will not be called. (default: 10)
--ploidy
Integer: 1 <= x <= 4 The maximum number of different alleles expected. (default: 2)
--variant-in-forward-reverse-reads
<Boolean> Variants should be supported by at least 5--variant-probability
Double: 0.0 < x <= 100.0 The probability that the variant is different from the reference sequence. Lowering this number will detect more variants. (default: 90.0)