.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH GUSTAF "1" "June 2017" "gustaf 2.3.1+dfsg-4" "User Commands"
.SH NAME
gustaf \- Gustaf \- Generic mUlti\-SpliT Alignment Finder: Tool for split\-read mapping allowing multiple splits.
.PP
SYNOPSIS
.IP
gustaf [OPTIONS] <GENOME FASTA FILE> <READ FASTA FILE>
gustaf [OPTIONS] <GENOME FASTA FILE> <READ FASTA FILE> <READ FASTA FILE 2>
.PP
DESCRIPTION
.IP
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.
.IP
The genome file is used as database input, the read file as query input.
.IP
All STELLAR options are supported. See STELLAR documentation for STELLAR
parameters and options.
.IP
(c) 2011\-2012 by Kathrin Trappe
.PP
REQUIRED ARGUMENTS
.IP
FASTA_FILE_1 INPUT_FILE
.IP
Valid filetypes are: .fq, .fastq, .fasta, and .fa.
.IP
FASTA_FILE_2 List of INPUT_FILE's
.IP
Either one (single\-end) or two (paired\-end) read files. Valid
filetypes are: .fq, .fastq, .fasta, and .fa.
.PP
OPTIONS
.HP
\fB\-h\fR, \fB\-\-help\fR
.IP
Display the help message.
.HP
\fB\-\-version\-check\fR BOOL
.IP
Turn this option off to disable version update notifications of the
application. One of 1, ON, TRUE, T, YES, 0, OFF, FALSE, F, and NO.
Default: 1.
.HP
\fB\-\-version\fR
.IP
Display version information.
.IP
Main Options:
.HP
\fB\-tp\fR, \fB\-\-transPen\fR INTEGER
.IP
Interchromosomal translocation penalty Default: 5.
.HP
\fB\-ip\fR, \fB\-\-invPen\fR INTEGER
.IP
Inversion penalty Default: 5.
.HP
\fB\-op\fR, \fB\-\-orderPen\fR INTEGER
.IP
Intrachromosomal order change penalty Default: 0.
.HP
\fB\-oth\fR, \fB\-\-overlapThresh\fR DOUBLE
.IP
Allowed overlap between matches Default: 0.5.
.HP
\fB\-gth\fR, \fB\-\-gapThresh\fR INTEGER
.IP
Allowed gap length between matches, default value corresponse to
expected size of microindels (5 bp) Default: 5.
.HP
\fB\-ith\fR, \fB\-\-initGapThresh\fR INTEGER
.IP
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.
.HP
\fB\-bth\fR, \fB\-\-breakendThresh\fR INTEGER
.IP
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.
.HP
\fB\-tth\fR, \fB\-\-tandemThresh\fR INTEGER
.IP
Minimal length of (small) insertion/duplication with double overlap
to be considered tandem repeat Default: 50.
.HP
\fB\-pth\fR, \fB\-\-breakpoint\-pos\-range\fR INTEGER
.IP
Allowed difference in breakpoint position Default: 5.
.HP
\fB\-cbp\fR, \fB\-\-complex\-breakpoints\fR
.IP
Disable inferring complex SVs
.HP
\fB\-st\fR, \fB\-\-support\fR INTEGER
.IP
Number of supporting reads Default: 2.
.HP
\fB\-mst\fR, \fB\-\-mate\-support\fR INTEGER
.IP
Number of supporting concordant mates Default: 2.
.HP
\fB\-ll\fR, \fB\-\-library\-size\fR INTEGER
.IP
Library size of paired\-end reads
.HP
\fB\-le\fR, \fB\-\-library\-error\fR INTEGER
.IP
Library error (sd) of paired\-end reads
.HP
\fB\-rc\fR, \fB\-\-revcompl\fR
.IP
Disable reverse complementing second mate pair input file.
.IP
Input Options:
.HP
\fB\-m\fR, \fB\-\-matchfile\fR INPUT_FILE
.IP
File of (stellar) matches Valid filetypes are: .gff and .GFF.
.IP
Output Options:
.HP
\fB\-gff\fR, \fB\-\-gffOut\fR OUTPUT_FILE
.IP
Name of gff breakpoint output file. Valid filetypes are: .txt and
\&.gff. Default: breakpoints.gff.
.HP
\fB\-vcf\fR, \fB\-\-vcfOut\fR OUTPUT_FILE
.IP
Name of vcf breakpoint output file. Valid filetypes are: .vcf and
\&.txt. Default: breakpoints.vcf.
.HP
\fB\-j\fR, \fB\-\-jobName\fR STRING
.IP
Job/Queue name Default: .
.HP
\fB\-do\fR, \fB\-\-dots\fR
.IP
Enable graph output in dot format
.IP
Parallelization Options:
.HP
\fB\-nth\fR, \fB\-\-numThreads\fR INTEGER
.IP
Number of threads for parallelization of I/O. Default: 1.
.IP
Main Options:
.HP
\fB\-e\fR, \fB\-\-epsilon\fR DOUBLE
.IP
Maximal error rate (max 0.25). In range [0.0000001..0.25]. Default:
0.05.
.HP
\fB\-l\fR, \fB\-\-minLength\fR INTEGER
.IP
Minimal length of epsilon\-matches. In range [0..inf]. Default: 100.
.HP
\fB\-f\fR, \fB\-\-forward\fR
.IP
Search only in forward strand of database.
.HP
\fB\-r\fR, \fB\-\-reverse\fR
.IP
Search only in reverse complement of database.
.HP
\fB\-a\fR, \fB\-\-alphabet\fR STRING
.IP
Alphabet type of input sequences (dna, rna, dna5, rna5, protein,
char). One of dna, dna5, rna, rna5, protein, and char.
.HP
\fB\-v\fR, \fB\-\-verbose\fR
.IP
Set verbosity mode.
.IP
Filtering Options:
.HP
\fB\-k\fR, \fB\-\-kmer\fR INTEGER
.IP
Length of the q\-grams (max 32). In range [1..32].
.HP
\fB\-rp\fR, \fB\-\-repeatPeriod\fR INTEGER
.IP
Maximal period of low complexity repeats to be filtered. Default: 1.
.HP
\fB\-rl\fR, \fB\-\-repeatLength\fR INTEGER
.IP
Minimal length of low complexity repeats to be filtered. Default:
1000.
.HP
\fB\-c\fR, \fB\-\-abundanceCut\fR DOUBLE
.IP
k\-mer overabundance cut ratio. In range [0..1]. Default: 1.
.IP
Verification Options:
.HP
\fB\-x\fR, \fB\-\-xDrop\fR DOUBLE
.IP
Maximal x\-drop for extension. Default: 5.
.HP
\fB\-vs\fR, \fB\-\-verification\fR STRING
.IP
Verification strategy: exact or bestLocal or bandedGlobal One of
exact, bestLocal, and bandedGlobal. Default: exact.
.HP
\fB\-dt\fR, \fB\-\-disableThresh\fR INTEGER
.IP
Maximal number of verified matches before disabling verification for
one query sequence (default infinity). In range [0..inf].
.HP
\fB\-n\fR, \fB\-\-numMatches\fR INTEGER
.IP
Maximal number of kept matches per query and database. If STELLAR
finds more matches, only the longest ones are kept. Default: 50.
.HP
\fB\-s\fR, \fB\-\-sortThresh\fR INTEGER
.IP
Number of matches triggering removal of duplicates. Choose a smaller
value for saving space. Default: 500.
.PP
VERSION
.IP
Last update: August 2014
gustaf version: 1.0.0
SeqAn version: 2.3.1