NAME

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

SYNOPSIS

       gustaf [OPTIONS] <GENOME FASTA FILE> <READ FASTA FILE>

       gustaf [OPTIONS] <GENOME FASTA FILE> <READ FASTA FILE> <READ FASTA FILE 2>

DESCRIPTION

       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

REQUIRED ARGUMENTS

       FASTA_FILE_1 INPUT_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.

OPTIONS

       -h, --help
              Display the help message.

       --version
              Display version information.

   Main Options:
       -tp, --transPen INTEGER
              Interchromosomal translocation penalty Default: 5.

       -ip, --invPen INTEGER
              Inversion penalty Default: 5.

       -op, --orderPen INTEGER
              Intrachromosomal order change penalty Default: 0.

       -oth, --overlapThresh DOUBLE
              Allowed overlap between matches Default: 0.5.

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

       -ith, --initGapThresh INTEGER
              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, --breakendThresh INTEGER
              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, --tandemThresh INTEGER
              Minimal length of (small) insertion/duplication with double overlap to be considered tandem repeat
              Default: 50.

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

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

       -st, --support INTEGER
              Number of supporting reads Default: 2.

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

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

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

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

   Input Options:
       -m, --matchfile INPUT_FILE
              File of (stellar) matches Valid filetypes are: .gff and .GFF.

   Output Options:
       -gff, --gffOut OUTPUT_FILE
              Name of gff breakpoint output file. Valid filetypes are: .txt and .gff. Default: breakpoints.gff.

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

       -j, --jobName STRING
              Job/Queue name Default: .

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

   Parallelization Options:
       -nth, --numThreads INTEGER
              Number of threads for parallelization of I/O. Default: 1.

   Main Options:
       -e, --epsilon DOUBLE
              Maximal error rate (max 0.25). In range [0.0000001..0.25]. Default: 0.05.

       -l, --minLength INTEGER
              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, --alphabet STRING
              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.

   Filtering Options:
       -k, --kmer INTEGER
              Length of the q-grams (max 32). In range [1..32].

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

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

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

   Verification Options:
       -x, --xDrop DOUBLE
              Maximal x-drop for extension. Default: 5.

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

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

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

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

gustaf 1.0.0                                       August 2014                                         GUSTAF(1)