Provided by: gmap_2012-06-12-1ubuntu1_amd64 
NAME
gmap - Genomic Mapping and Alignment Program
SYNOPSIS
gmap -dDB|-gFASTA [OPTION]... [QUERY]...
DESCRIPTION
Align the sequences QUERY to the reference, specified with -d or -g. With no QUERY, read
standard input.
OPTIONS
Input options
-D, --dir=directory
Genome directory
-d, --db=STRING
Genome database. If argument is '?' (with the quotes), this command lists available
databases.
-k, --kmer=INT
kmer size to use in genome database (allowed values: 16 or less). If not
specified, the program will find the highest available kmer size in the genome
database
--basesize=INT
Base size to use in genome database. If not specified, the program will find the
highest available base size in the genome database within selected k-mer size
--sampling=INT
Sampling to use in genome database. If not specified, the program will find the
smallest available sampling value in the genome database within selected basesize
and k-mer size
-G, --genomefull
Use full genome (all ASCII chars allowed; built explicitly during setup), not
compressed version
-g, --gseg=filename
User-supplied genomic segment
-1, --selfalign
Align one sequence against itself in FASTA format via stdin (Useful for getting
protein translation of a nucleotide sequence)
-2, --pairalign
Align two sequences in FASTA format via stdin, first one being genomic and second
one being cDNA
--cmdline=STRING,STRING
Align these two sequences provided on the command line, first one being genomic and
second one being cDNA
-q, --part=INT/INT
Process only the i-th out of every n sequences e.g., 0/100 or 99/100 (useful for
distributing jobs to a computer farm).
--input-buffer=INT
Size of input buffer (program reads this many sequences at a time for efficiency)
(default 1000)
Computation options
-B, --batch=INT
Mode Offsets Positions Genome
0 allocate mmap mmap
1 allocate mmap & preload mmap
2 allocate mmap & preload mmap & preload (default)
3 allocate allocate mmap & preload
4 allocate allocate allocate
5 expand allocate allocate
Note: For a single sequence, all data structures use mmap. If mmap not available
and allocate not chosen, then will use fileio (very slow)
--nosplicing
Turns off splicing (useful for aligning genomic sequences onto a genome)
--min-intronlength=INT
Min length for one internal intron (default 9). Below this size, a genomic gap
will be considered a deletion rather than an intron.
-K, --intronlength=INT
Max length for one internal intron (default 1000000)
-w, --localsplicedist=INT
Max length for known splice sites at ends of sequence (default 200000)
-L, --totallength=INT
Max total intron length (default 2400000)
-x, --chimera-margin=INT
Amount of unaligned sequence that triggers search for the remaining sequence
(default 40). Enables alignment of chimeric reads, and may help with some non-
chimeric reads. To turn off, set to a large value (greater than the query length).
-t, --nthreads=INT
Number of worker threads
-C, --chrsubsetfile=filename
User-supplied chromosome subset file
-c, --chrsubset=string
Chromosome subset to search
-z, --direction=STRING
cDNA direction (sense_force, antisense_force, sense_filter, antisense_filter, or
auto (default))
-H, --trimendexons=INT
Trim end exons with fewer than given number of matches (in nt, default 12)
--cross-species
For cross-species alignments, use a more sensitive search for canonical splicing
--canonical-mode=INT
Reward for canonical and semi-canonical introns 0=low reward, 1=high reward
(default), 2=low reward for high-identity sequences and high reward otherwise
--allow-close-indels=INT
Allow an insertion and deletion close to each other (0=no, 1=yes (default), 2=only
for high-quality alignments)
--microexon-spliceprob=FLOAT
Allow microexons only if one of the splice site probabilities is greater than this
value (default 0.90)
--cmetdir=STRING
Directory for methylcytosine index files (created using cmetindex) (default is
location of genome index files specified using -D, -V, and -d)
--atoidir=STRING
Directory for A-to-I RNA editing index files (created using atoiindex) (default is
location of genome index files specified using -D, -V, and -d)
--mode=STRING
Alignment mode: standard (default), cmet-stranded, cmet-nonstranded, atoi-stranded,
or atoi-nonstranded. Non-standard modes requires you to have previously run the
cmetindex or atoiindex programs on the genome
-p, --prunelevel
Pruning level: 0=no pruning (default), 1=poor seqs, 2=repetitive seqs, 3=poor and
repetitive
Output types
-S, --summary
Show summary of alignments only
-A, --align
Show alignments
-3, --continuous
Show alignment in three continuous lines
-4, --continuous-by-exon
Show alignment in three lines per exon
-Z, --compress
Print output in compressed format
-E, --exons=STRING
Print exons ("cdna" or "genomic")
-P, --protein_dna
Print protein sequence (cDNA)
-Q, --protein_gen
Print protein sequence (genomic)
-f, --format=INT
Other format for output (also note the -A and -S options and other options listed
under Output types):
psl (or 1)= PSL (BLAT) format,
gff3_gene (or 2)= GFF3 gene format,
gff3_match_cdna (or 3)= GFF3 cDNA_match format,
gff3_match_est (or 4) = GFF3 EST_match format,
splicesites (or 6) = splicesites output (for GSNAP splicing file),
introns = introns output (for GSNAP splicing file),
map_exons (or 7) = IIT FASTA exon map format,
map_genes (or 8) = IIT FASTA map format,
coords (or 9) = coords in table format,
sampe = SAM format (setting paired_read bit in flag),
samse = SAM format (without setting paired_read bit)
Output options
-n, --npaths=INT
Maximum number of paths to show. If set to 0, prints two paths if chimera detected,
else one.
--quiet-if-excessive
If more than maximum number of paths are found, then nothing is printed.
--suboptimal-score=INT
Report only paths whose score is within this value of the best path. By default, if
this option is not provided, the program prints all paths found.
-O, --ordered
Print output in same order as input (relevant only if there is more than one worker
thread)
-5, --md5
Print MD5 checksum for each query sequence
-o, --chimera-overlap
Overlap to show, if any, at chimera breakpoint
--failsonly
Print only failed alignments, those with no results
--nofails
Exclude printing of failed alignments
--fails-as-input
Print completely failed alignments as input FASTA or FASTQ format
-V, --usesnps=STRING
Use database containing known SNPs (in <STRING>.iit, built previously using
snpindex) for reporting output
--split-output=STRING
Basename for multiple-file output, separately for nomapping, uniq, mult, (and
chimera, if --chimera-margin is selected)
--output-buffer-size=INT
Buffer size, in queries, for output thread (default 1000). When the number of
results to be printed exceeds this size, the worker threads are halted until the
backlog is cleared
-F, --fulllength
Assume full-length protein, starting with Met
--cdsstart=INT
Translate codons from given nucleotide (1-based)
-T, --truncate
Truncate alignment around full-length protein, Met to Stop Implies -F flag.
-Y, --tolerant
Translates cDNA with corrections for frameshifts
Options for SAM output
--no-sam-headers
Do not print headers beginning with '@'
--sam-use-0M
Insert 0M in CIGAR between adjacent insertions and deletions Required by Picard,
but can cause errors in other tools
--read-group-id=STRING
Value to put into read-group id (RG-ID) field
--read-group-name=STRING
Value to put into read-group name (RG-SM) field
--read-group-library=STRING
Value to put into read-group library (RG-LB) field
--read-group-platform=STRING
Value to put into read-group library (RG-PL) field
Options for quality scores
--quality-protocol=STRING
Protocol for input quality scores. Allowed values:
illumina (ASCII 64-126) (equivalent to -J 64 -j -31)
sanger (ASCII 33-126) (equivalent to -J 33 -j 0)
Default is sanger (no quality print shift) SAM output files should have quality
scores in sanger protocol. Or you can specify the print shift with this flag:
-j, --quality-print-shift=INT
Shift FASTQ quality scores by this amount in output (default is 0 for sanger
protocol; to change Illumina input to Sanger output, select -31)
External map file options
-M, --mapdir=directory
Map directory
-m, --map=iitfile
Map file. If argument is '?' (with the quotes), this lists available map files.
-e, --mapexons
Map each exon separately
-b, --mapboth
Report hits from both strands of genome
-u, --flanking=INT
Show flanking hits (default 0)
--print-comment
Show comment line for each hit
Alignment output options
-N, --nolengths
No intron lengths in alignment
-I, --invertmode=INT
Mode for alignments to genomic (-) strand:
0=Don't invert the cDNA (default)
1=Invert cDNA and print genomic (-) strand
2=Invert cDNA and print genomic (+) strand
-i, --introngap=INT
Nucleotides to show on each end of intron (default=3)
-l, --wraplength=INT
Wrap length for alignment (default=50)
Help options
--version
Show version
--help Show this help message
ENVIRONMENT
GMAPDB genome directory (eqivalent to -D)
FILES
~/.gmaprc
configuration file
AUTHOR
Thomas D. Wu and Colin K. Watanabe
REPORTING BUGS
Report bugs to Thomas Wu <twu@gene.com>.
COPYRIGHT
Copyright 2005 Genentech, Inc. All rights reserved.
SEE ALSO
gmap_setup(1), gsnap(1)
http://research-pub.gene.com/gmap/