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gmap - Genomic Mapping and Alignment Program

GMAP(1) User Commands GMAP(1)

NAME

gmap - Genomic Mapping and Alignment Program

SYNOPSIS

gmap [ OPTIONS...] <FASTA files...>, or cat <FASTA files...> | gmap [OPTIONS...]

OPTIONS

Input options (must include -d or -g)

-D, --dir=directory
Genome directory. Default (as specified by --with-gmapdb to the configure program) is /var/cache/gmap
-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
--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 k-mer size
-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-size=INT
Size of input buffer (program reads this many sequences at a time for efficiency) (default 1000)
Computation options
-B, --batch=INT
Batch mode (default = 2)
 

Mode Offsets Positions Genome
0 see note mmap mmap
1 see note mmap & preload mmap
(default) 2 see note mmap & preload mmap & preload
3 see note allocate mmap & preload
4 see note 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)
Note about --batch and offsets: Expansion of offsets can be controlled
independently by the --expand-offsets flag. The --batch= 5 option is equivalent to --batch=4 plus --expand-offsets=1
--expand-offsets=INT
Whether to expand the genomic offsets index Values: 0 (no, default), or 1 (yes). Expansion gives faster alignment, but requires more memory
--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.
--max-intronlength-middle=INT
Max length for one internal intron (default 500000). Note: for backward compatibility, the -K or --intronlength flag will set both --max-intronlength-middle and --max-intronlength-ends. Also see --split-large-introns below.
--max-intronlength-ends=INT
Max length for first or last intron (default 10000). Note: for backward compatibility, the -K or --intronlength flag will set both --max-intronlength-middle and --max-intronlength-ends.
--split-large-introns
Sometimes GMAP will exceed the value for --max-intronlength-middle, if it finds a good single alignment. However, you can force GMAP to split such alignments by using this flag
--trim-end-exons=INT
Trim end exons with fewer than given number of matches (in nt, default 12)
-w, --localsplicedist=INT
Max length for known splice sites at ends of sequence (default 2000000)
-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 30). Enables alignment of chimeric reads, and may help with some non-chimeric reads. To turn off, set to zero.
--no-chimeras
Turns off finding of chimeras. Same effect as --chimera-margin= 0
-t, --nthreads=INT
Number of worker threads
-c, --chrsubset=string
Limit search to given chromosome
-z, --direction=STRING
cDNA direction (sense_force, antisense_force, sense_filter, antisense_filter,or auto (default))
--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
--cross-species
Use a more sensitive search for canonical splicing, which helps especially for cross-species alignments and other difficult cases
--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 0.95)
--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, atoi-nonstranded, ttoc-stranded, or ttoc-nonstranded. Non-standard modes requires you to have previously run the cmetindex or atoiindex programs (which also cover the ttoc modes) 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_ranges (or 8) = IIT FASTA range 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),
bedpe = indels and gaps in BEDPE format
Output options
-n, --npaths=INT
Maximum number of paths to show (default 5). If set to 1, GMAP will not report chimeric alignments, since those imply two paths. If you want a single alignment plus chimeric alignments, then set this to be 0.
--suboptimal-score=FLOAT
Report only paths whose score is within this value of the best path.
If specified between 0.0 and 1.0, then treated as a fraction
of the score of the best alignment (matches minus penalties for mismatches and indels). Otherwise, treated as an integer number to be subtracted from the score of the best alignment. Default value is 0.50.
-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
-V, --snpsdir=STRING
Directory for SNPs index files (created using snpindex) (default is location of genome index files specified using -D and -d)
-v, --use-snps=STRING
Use database containing known SNPs (in <STRING>.iit, built previously using snpindex) for tolerance to SNPs
--split-output=STRING
Basename for multiple-file output, separately for nomapping,
uniq, mult, (and chimera, if --chimera-margin is selected)
--failed-input=STRING
Print completely failed alignments as input FASTA or FASTQ format to the given file. If the --split-output flag is also given, this file is generated in addition to the output in the .nomapping file.
--append-output
When --split-output or --failedinput is given, this flag will append output to the existing files. Otherwise, the default is to create new files.
--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
--translation-code=INT
Genetic code used for translating codons to amino acids and computing CDS Integer value (default=1) corresponds to an available code at http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi
--alt-start-codons
Also, use the alternate initiation codons shown in the above Web site By default, without this option, only ATG is considered an initiation codon
-F, --fulllength
Assume full-length protein, starting with Met
-a, --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 GFF3 output
--gff3-add-separators=INT
Whether to add a ### separator after each query sequence Values: 0 (no), 1 (yes, default)
--gff3-swap-phase=INT
Whether to swap phase (0 => 0, 1 => 2, 2 => 1) in gff3_gene format Needed by some analysis programs, but deviates from GFF3 specification Values: 0 (no, default), 1 (yes)
--gff3-cds=STRING
Whether to use cDNA or genomic translation for the CDS coordinates Values: cdna (default), genomic
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
--sam-extended-cigar
Use extended CIGAR format (using X and = symbols instead of M,
to indicate matches and mismatches, respectively
--force-xs-dir
For RNA-Seq alignments, disallows XS:A:? when the sense direction is unclear, and replaces this value arbitrarily with XS:A:+. May be useful for some programs, such as Cufflinks, that cannot handle XS:A:?. However, if you use this flag, the reported value of XS:A:+ in these cases will not be meaningful.
--md-lowercase-snp
In MD string, when known SNPs are given by the -v flag,
prints difference nucleotides as lower-case when they,
differ from reference but match a known alternate allele
--action-if-cigar-error
Action to take if there is a disagreement between CIGAR length and sequence length Allowed values: ignore, warning (default), abort
--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)
Filtering output options
--min-trimmed-coverage=FLOAT
Do not print alignments with trimmed coverage less this value (default=0.0, which means no filtering) Note that chimeric alignments will be output regardless of this filter
--min-identity=FLOAT
Do not print alignments with identity less this value (default=0.0, which means no filtering) Note that chimeric alignments will be output regardless of this filter Help options
--check
Check compiler assumptions
--version
Show version
--help
Show this help message
 
Other tools of GMAP suite are located in /usr/lib/gmap
October 2017 gmap 2017-10-12-1