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GMAP(1) User Commands GMAP(1)


gmap - Genomic Mapping and Alignment Program


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


Input options (must include -d or -g)

Genome directory. Default (as specified by --with-gmapdb to the configure program) is /var/cache/gmap
Genome database. If argument is '?' (with the quotes), this command lists available databases.
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 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
User-supplied genomic segments. If multiple segments are provided, then every query sequence is aligned against every 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
Align these two sequences provided on the command line, first one being genomic and second one being cDNA
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).
Size of input buffer (program reads this many sequences at a time for efficiency) (default 1000)

Computation options

Batch mode (default = 2)

Mode Positions Genome
0 mmap mmap
1 mmap & preload mmap
(default) 2 mmap & preload mmap & preload
3 allocate mmap & preload
4 allocate allocate
5 allocate allocate (same as 4)

If mmap not available and allocate not chosen, then will use fileio (very slow)
If 1, then allocated memory is shared among all processes on this node If 0 (default), then each process has private allocated memory
Turns off splicing (useful for aligning genomic sequences onto a genome)
Max length for a deletion (default 100). Above this size, a genomic gap will be considered an intron rather than a deletion. If the genomic gap is less than --max-deletionlength and greater than --min-intronlength, a known splice site or splice site probabilities of 0.80 on both sides will be reported as an intron.
Min length for one internal intron (default 9). Below this size, a genomic gap will be considered a deletion rather than an intron. If the genomic gap is less than --max-deletionlength and greater than --min-intronlength, a known splice site or splice site probabilities of 0.80 on both sides will be reported as an intron.
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 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.
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 ends if the alignment score is below this value where a match scores +1 and a mismatch scores -3 The value should be 0 (default) or negative. A negative allows some mismatches at the ends of the alignment
Trim end exons with fewer than given number of matches (in nt, default 12)
Max length for known splice sites at ends of sequence (default 2000000)
Max total intron length (default 2400000)
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.
Turns off finding of chimeras. Same effect as --chimera-margin=0
Number of worker threads
Limit search to given chromosome
Genome strand to try aligning to (plus, minus, or both default)
cDNA direction (sense_force, antisense_force, sense_filter, antisense_filter,or auto (default))
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
Use a more sensitive search for canonical splicing, which helps especially for cross-species alignments and other difficult cases
Allow an insertion and deletion close to each other (0=no, 1=yes (default), 2=only for high-quality alignments)
Allow microexons only if one of the splice site probabilities is greater than this value (default 0.95)
In dynamic programming, opening penalty for indel
In dynamic programming, extension penalty for indel Values for --indel-open and --indel-extend should be in [-127,-1]. If value is < -127, then will use -127 instead. If --indel-open and --indel-extend are not specified, values are chosen adaptively, based on the differences between the query and reference
Directory for methylcytosine index files (created using cmetindex) (default is location of genome index files specified using -D, -V, and -d)
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)
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
Pruning level: 0=no pruning (default), 1=poor seqs, 2=repetitive seqs, 3=poor and repetitive

Output types

Show summary of alignments only
Show alignments
-3, --continuous
Show alignment in three continuous lines
-4, --continuous-by-exon
Show alignment in three lines per exon
Print exons ("cdna" or "genomic") Will also print introns with "cdna+introns" or "genomic+introns"
Print protein sequence (cDNA)
Print protein sequence (genomic)
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

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.
Report only paths whose score is within this value of the best path.
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.
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
Overlap to show, if any, at chimera breakpoint
Print only failed alignments, those with no results
Exclude printing of failed alignments
Directory for SNPs index files (created using snpindex) (default is location of genome index files specified using -D and -d)
Use database containing known SNPs (in <STRING>.iit, built previously using snpindex) for tolerance to SNPs
Basename for multiple-file output, separately for nomapping,
uniq, mult, (and chimera, if --chimera-margin is selected)
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.
When --split-output or --failedinput is given, this flag will append output to the existing files. Otherwise, the default is to create new files.
Buffer size, in queries, for output thread (default 1000). When the number of results to be printed exceeds this size, worker threads wait until the backlog is cleared
Genetic code used for translating codons to amino acids and computing CDS Integer value (default=1) corresponds to an available code at
Also, use the alternate initiation codons shown in the above Web site By default, without this option, only ATG is considered an initiation codon
Assume full-length protein, starting with Met
Translate codons from given nucleotide (1-based)
Truncate alignment around full-length protein, Met to Stop Implies -F flag.
Translates cDNA with corrections for frameshifts

Options for GFF3 output

Whether to add a ### separator after each query sequence Values: 0 (no), 1 (yes, default)
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)
Whether to include annotation from the FASTA header into the GFF3 output Values: 0 (default): Do not include
1: Wrap all annotation as Annot="<header>"
2: Include key=value pairs, replacing brackets with quotation marks
and replacing spaces between key=value pairs with semicolons
Whether to use cDNA or genomic translation for the CDS coordinates Values: cdna (default), genomic

Options for SAM output

Do not print headers beginning with '@'
Insert 0M in CIGAR between adjacent insertions and deletions Required by Picard, but can cause errors in other tools
Use extended CIGAR format (using X and = symbols instead of M,
to indicate matches and mismatches, respectively
Flip the query and genomic positions in the SAM output. Potentially useful with the -g flag when short reads are picked as query sequences and longer reads as picked as genomic sequences
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.
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 to take if there is a disagreement between CIGAR length and sequence length Allowed values: ignore, warning (default), noprint, abort Note that the noprint option does not print the CIGAR string at all if there is an error, so it may break a SAM parser
Value to put into read-group id (RG-ID) field
Value to put into read-group name (RG-SM) field
Value to put into read-group library (RG-LB) field
Value to put into read-group library (RG-PL) field

Options for quality scores

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)
SAM output files should have quality scores in sanger protocol
Or you can specify the print shift with this flag:
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

Map directory
Map file. If argument is '?' (with the quotes),
this lists available map files.
Map each exon separately
Report hits from both strands of genome
Show flanking hits (default 0)
Show comment line for each hit

Alignment output options

No intron lengths in alignment
No left margin in GMAP standard output (with the -A flag)
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
Nucleotides to show on each end of intron (default 3)
Wrap length for alignment (default 50)

Filtering output options

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
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 compiler assumptions
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October 2022 gmap 2021-12-17+ds-3