GUSTAF(1)

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.