The available options for the DiscoverySNPCallerPlugin are as follows:
-i       Input .tbt file
-y       Use byte-formatted TBT file (*.tbt.byte)
-m       TagsOnPhysicalMap file containing genomic positions of tags
-mUpd    Update TagsOnPhysicalMap file with allele calls for Production Pipeline, save to specified file (default: no updating)
-o       Output HapMap file. Use a plus sign (+) as a wild card character in place of the chromosome number
           (e.g., /path/hapmap/myGBSGenos.chr+.hmp.txt)
-vcf     Output a VCF file (*.vcf) as well as the default HapMap (*.hmp.txt)  (default: false)
-mxSites Maximum number of sites (SNPs) output per chromosome (default: 200000)
-mnF     Minimum F (inbreeding coefficient) (default: 0.8  = no filter)
-p       Pedigree file containing full sample names (or expected names after merging) & expected inbreeding
         coefficient (F) for each.  Only taxa with expected F >= mnF used to calculate F = 1-Ho/He.
         (default: use ALL taxa to calculate F)
-mnMAF   Minimum minor allele frequency (default: 0.01)
-mnMAC   Minimum minor allele count (default: 10)
-mnLCov  Minimum locus coverage (proportion of Taxa with a genotype) (default: 0.1)
-errRate Average sequencing error rate per base (used to decide between heterozygous and homozygous calls) (default: 0.01)
-ref     Path to reference genome in fasta format. Ensures that a tag from the reference genome is always included
         when the tags at a locus are aligned against each other to call SNPs. The reference allele for each site
         is then provided in the output HapMap files, under the taxon name "REFERENCE_GENOME" (first taxon).
         DEFAULT: Don't use reference genome.
-inclRare  Include the rare alleles at site (3 or 4th states) (default: false)
-inclGaps  Include sites where major or minor allele is a GAP (default: false)
-callBiSNPsWGap  Include sites where the third allele is a GAP (default: false) (mutually exclusive with inclGaps)
-sC       Start chromosome
-eC       End chromosome