NAME¶

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-check BOOL

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.

--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.

VERSION

Last update: August 2014 gustaf version: 1.0.0 SeqAn version: 2.3.1