gustaf - Gustaf - Generic mUlti-SpliT Alignment Finder: Tool for split-read mapping allowing multiple

       GUSTAF uses SeqAns STELLAR to find splits as local matches on different strands or chromosomes.  Criteria
       and  penalties  to  chain  these matches can be specified. Output file contains the breakpoints along the
       best chain.

       The genome file is used as database input, the read file as query input.

       All STELLAR options are supported. See STELLAR documentation for STELLAR parameters and options.

       (c) 2011-2012 by Kathrin Trappe

       gustaf  -  Gustaf  -  Generic mUlti-SpliT Alignment Finder: Tool for split-read mapping allowing multiple
       splits.

-h, --help
              Display the help message.

       --version
              Display version information.

   MainOptions:-tp, --transPenINTEGER
              Interchromosomal translocation penalty Default: 5.

       -ip, --invPenINTEGER
              Inversion penalty Default: 5.

       -op, --orderPenINTEGER
              Intrachromosomal order change penalty Default: 0.

       -oth, --overlapThreshDOUBLE
              Allowed overlap between matches Default: 0.5.

       -gth, --gapThreshINTEGER
              Allowed  gap  length between matches, default value corresponse to expected size of microindels (5
              bp) Default: 5.

       -ith, --initGapThreshINTEGER
              Allowed initial or ending gap length at begin and end of read with  no  breakpoint  (e.g.  due  to
              sequencing errors at the end) Default: 15.

       -bth, --breakendThreshINTEGER
              Allowed  initial  or ending gap length at begin and end of read that creates a breakend/breakpoint
              (e.g. for reads extending into insertions) Default: 30.

       -tth, --tandemThreshINTEGER
              Minimal length of (small) insertion/duplication with double overlap to be considered tandem repeat
              Default: 50.

       -pth, --breakpoint-pos-rangeINTEGER
              Allowed difference in breakpoint position Default: 5.

       -cbp, --complex-breakpoints
              Disable inferring complex SVs

       -st, --supportINTEGER
              Number of supporting reads Default: 2.

       -mst, --mate-supportINTEGER
              Number of supporting concordant mates Default: 2.

       -ll, --library-sizeINTEGER
              Library size of paired-end reads

       -le, --library-errorINTEGER
              Library error (sd) of paired-end reads

       -rc, --revcompl
              Disable reverse complementing second mate pair input file.

   InputOptions:-m, --matchfileINPUT_FILE
              File of (stellar) matches Valid filetypes are: .gff and .GFF.

   OutputOptions:-gff, --gffOutOUTPUT_FILE
              Name of gff breakpoint output file. Valid filetypes are: .txt and .gff. Default: breakpoints.gff.

       -vcf, --vcfOutOUTPUT_FILE
              Name of vcf breakpoint output file. Valid filetypes are: .vcf and .txt. Default: breakpoints.vcf.

       -j, --jobNameSTRING
              Job/Queue name Default: .

       -do, --dots
              Enable graph output in dot format

   ParallelizationOptions:-nth, --numThreadsINTEGER
              Number of threads for parallelization of I/O. Default: 1.

   MainOptions:-e, --epsilonDOUBLE
              Maximal error rate (max 0.25). In range [0.0000001..0.25]. Default: 0.05.

       -l, --minLengthINTEGER
              Minimal length of epsilon-matches. In range [0..inf]. Default: 100.

       -f, --forward
              Search only in forward strand of database.

       -r, --reverse
              Search only in reverse complement of database.

       -a, --alphabetSTRING
              Alphabet type of input sequences (dna, rna, dna5, rna5, protein, char). One  of  dna,  dna5,  rna,
              rna5, protein, and char.

       -v, --verbose
              Set verbosity mode.

   FilteringOptions:-k, --kmerINTEGER
              Length of the q-grams (max 32). In range [1..32].

       -rp, --repeatPeriodINTEGER
              Maximal period of low complexity repeats to be filtered. Default: 1.

       -rl, --repeatLengthINTEGER
              Minimal length of low complexity repeats to be filtered. Default: 1000.

       -c, --abundanceCutDOUBLE
              k-mer overabundance cut ratio. In range [0..1]. Default: 1.

   VerificationOptions:-x, --xDropDOUBLE
              Maximal x-drop for extension. Default: 5.

       -vs, --verificationSTRING
              Verification   strategy:  exact  or  bestLocal  or  bandedGlobal  One  of  exact,  bestLocal,  and
              bandedGlobal. Default: exact.

       -dt, --disableThreshINTEGER
              Maximal number of verified matches before disabling verification for one query  sequence  (default
              infinity). In range [0..inf].

       -n, --numMatchesINTEGER
              Maximal  number  of  kept  matches per query and database. If STELLAR finds more matches, only the
              longest ones are kept. Default: 50.

       -s, --sortThreshINTEGER
              Number of matches triggering removal of duplicates. Choose  a  smaller  value  for  saving  space.
              Default: 500.

gustaf 1.0.0                                       August 2014                                         GUSTAF(1)

FASTA_FILE_1INPUT_FILE
               Valid filetypes are: .fq, .fastq, .fasta, and .fa.

       FASTA_FILE_2 List of INPUT_FILE's
              Either one (single-end) or two (paired-end) read files. Valid filetypes are: .fq, .fastq,  .fasta,
              and .fa.

gustaf [OPTIONS] <GENOMEFASTAFILE> <READFASTAFILE>

       gustaf [OPTIONS] <GENOMEFASTAFILE> <READFASTAFILE> <READFASTAFILE2>