gustaf - Gustaf - Generic mUlti-SpliT Alignment Finder: Tool for
split-read mapping allowing multiple splits.
gustaf [OPTIONS] <GENOME FASTA FILE>
<READ FASTA FILE>
gustaf [OPTIONS] <GENOME FASTA FILE>
<READ FASTA FILE> <READ FASTA FILE 2>
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
- -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.
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.
- -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.