vcf

--complex-represent <String> Allelic variants that overlap but do not cover the same range are called complex variants. These can be represented in different ways (see manual for details): Reference overlap: Accurate representation where reference alleles are added to the genotype field to specify complex overlapping alleles. Reference overlap and depth estimate: More widely compatible and less accurate representation. Star alleles: Accurate representation where star alleles are used to specify complex overlapping alleles. Without overlap specification: The legacy representation where complex overlap does not affect how variants are specified. (default: Reference overlap)
--compression <[NONE, GZIP, ZIP]> By selecting e.g. zip or gzip the exported result will be compressed (default: NONE)
-d, --destination <ClcFileUrl> The destination to export the files to
 
--enforce-ploidy <Boolean> Modify the VCF genotype field to reflect assumptions on minimum and maximum ploidy. A fixed ploidy of 2 can be achieved by setting both the Minimum ploidy and the Maximum ploidy to 2. (default: false)
--exclude-from-enforce-min-ploidy <String> Select one or more chromosomes which minimum ploidy should not apply to (e.g. male X and Y, and MT for humans).
--filenamepattern <String> Placeholders available for defining custom export file names are: * input or 1 - default name of the data element being exported * extension or 2 - default extension for the chosen format * counter or 3 - incremented number, useful when exporting multiple files * host - name of the machine the job is run on * user - name of the user who launched the job * year, month, day, hour, minute, and second - timestamp information based on the time an output is created. (default: input.extension)
-i, --input <ClcObjectUrl> Input data on server
--log <Boolean> Enable creation of algo log file. (default: false)
--max-ploidy  
Integer: 1 <= x <= 2147483647 Maximum number of alleles to be written in the genotype field of the VCF. When exporting variants with a higher number of alleles than the specified maximum ploidy, only the alleles with highest frequency, up to the specified maximum ploidy, will be written. (default: 2)
--min-ploidy  
Integer: 0 <= x <= 2147483647 Minimum number of alleles to be written in the genotype field of the VCF. In cases where fewer alleles are present, missing alleles are assumed to be represented by the most frequent allele. (default: 2)
--minimum-allele-fraction-threshold  
Double: 0.0 <= x <= 1.0 Only alleles with allele fraction above this threshold are considered as contributing to the minimum ploidy alleles. Alleles with a fraction below the threshold may still be reported in the VCF genotype field, if the Remove alleles below fraction threshold option is disabled and the maximum ploidy allows it. For example, with a maximum ploidy of 4 and minimum of 2, and three alleles where one (A) is above the threshold and two (C and T) are below the threshold, the VCF genotype field becomes A/A/C/T. If the Remove alleles below fraction threshold option is enabled, or the maximum ploidy is set to 2, the VCF genotype field becomes A/A. For further details see the manual. (default: 0.0)
--reference-track <ClcObjectUrl> Reference sequence track
--remove-alleles-below-fraction-threshold <Boolean> Removes alleles with fraction below Minimum allele fraction threshold. If this option is disabled, then Enforce minimum ploidy will not remove any alleles from the VCF genotype field. (default: true)