Provided by: gmap_2024-11-20+ds-2_amd64 
NAME
gsnapl - Large Genome Short-read Nucleotide Alignment Program
SYNOPSIS
gsnap [OPTIONS...] <FASTA file>, or cat <FASTA file> | gmap [OPTIONS...]
OPTIONS
Input options (must include -d)
-D, --dir=directory
Genome directory. Default (as specified by --with-gmapdb to the configure program) is
/var/cache/gmap
-d, --db=STRING
Genome database
--two-pass
Two-pass mode, in which the sequences are processed first to identify splice sites and introns,
and then aligned using this splicing information
--use-localdb=INT
Whether to use the local suffix arrays, which help with finding extensions to the ends of
alignments in the presence of splicing or indels (0=no, 1=yes if available (default))
Transcriptome-guided options (optional)
-C, --transcriptdir=directory
Transcriptome directory. Default is the value for --dir above
-c, --transcriptdb=STRING
Transcriptome database
--transcriptome-mode=STRING
Options: assist, only, annotate (default). The option assist means to try transcriptome alignment
first, but then use genomic alignment if nothing is found. The option only means to try
transcriptome alignment only. The option annotate means to try only genomic alignment, to use the
transcriptome only for annotation; this is the fastest option. In the other two options,
annotation is also performed
Computation options
-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
--align-fraction=FLOAT
Process only the given fraction of reads, selected at random If --align-fraction and --part are
given, --align-fraction takes precedence
-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 10000)
--barcode-length=INT
Amount of barcode to remove from start of every read before alignment (default 0)
--endtrim-length=INT
Amount of trim to remove from the end of every read before alignment (default 0)
--orientation=STRING
Orientation of paired-end reads Allowed values: FR (fwd-rev, or typical Illumina; default), RF
(rev-fwd, for circularized inserts), or FF (fwd-fwd, same strand), or 10X (single-cell where read
1 has barcode information; read 2 is rev)
--10x-whitelist=FILE
Whitelist of 10X Genomics GEM bead barcodes, needed to perform correction of cellular barcodes.
This file can be obtained at cellranger-x.y.z/lib/python/cellranger/barcodes (for Cell Ranger
version >= 4) cellranger-x.y.z/lib/cellranger-cs/x.y.z/lib/python/cellranger/barcodes (<= 3)
--10x-well-position=INT
Position of well information in the accession, when separated by colons If set to 0, then no well
information will be printed in the CB field (default: 4)
--fastq-id-start=INT
Starting position of identifier in FASTQ header, space-delimited (>= 1)
--fastq-id-end=INT
Ending position of identifier in FASTQ header, space-delimited (>= 1)
Examples:
@HWUSI-EAS100R:6:73:941:1973#0/1
start=1, end=1 (default) => identifier is HWUSI-EAS100R:6:73:941:1973#0
@SRR001666.1 071112_SLXA-EAS1_s_7:5:1:817:345 length=36
start=1, end=1 => identifier is SRR001666.1 start=2, end=2 => identifier is
071112_SLXA-EAS1_s_7:5:1:817:345 start=1, end=2 => identifier is SRR001666.1
071112_SLXA-EAS1_s_7:5:1:817:345
--force-single-end
When multiple FASTQ files are provided on the command line, GSNAP assumes they are matching
paired-end files. This flag treats each file as single-end.
--filter-chastity=STRING
Skips reads marked by the Illumina chastity program. Expecting a string after the accession
having a 'Y' after the first colon, like this:
@accession 1:Y:0:CTTGTA
where the 'Y' signifies filtering by chastity. Values: off (default), either, both. For
'either', a 'Y' on either end of a paired-end read will be filtered. For 'both', a 'Y' is
required on both ends of a paired-end read (or on the only end of a single-end read).
--allow-pe-name-mismatch
Allows accession names of reads to mismatch in paired-end files
--interleaved
Input is in interleaved format (one read per line, tab-delimited
--gunzip
Uncompress gzipped input files
--bunzip2
Uncompress bzip2-compressed input files
Computation options
-B, --batch=INT
Batch mode (default = 5) Mode Hash offsets Hash positions Genome Local hash offsets
Local hash positions Localdb
0 allocate mmap mmap allocate mmap mmap
1 allocate mmap & preload mmap allocate mmap & preload mmap
2 allocate mmap & preload mmap & preload allocate mmap & preload mmap
3 allocate allocate mmap & preload allocate allocate mmap
4 allocate allocate allocate allocate allocate mmap
(default)
5 allocate allocate allocate allocate allocate
allocate
Note: For a single sequence, all data structures use mmap
A batch level of 5 means the same as 4, and is kept only for backward compatibility
--use-shared-memory=INT
If 1, then allocated memory is shared among all processes on this node If 0 (default), then each
process has private allocated memory
--preload-shared-memory
Load files indicated by --batch mode into shared memory for use by other GMAP/GSNAP processes on
this node, and then exit. Ignore any input files.
--unload-shared-memory
Unload files indicated by --batch mode into shared memory, or allow them to be unloaded when
existing GMAP/GSNAP processes on this node are finished with them. Ignore any input files.
-m, --max-mismatches=FLOAT
Maximum number of mismatches allowed (if not specified, then GSNAP tries to find the best possible
match in the genome) If specified between 0.0 and 1.0, then treated as a fraction of each read
length. Otherwise, treated as an integral number of mismatches (including indel and splicing
penalties). Default is 0.3
--query-unk-mismatch=INT
Whether to count unknown (N) characters in the query as a mismatch (0=no (default), 1=yes)
--genome-unk-mismatch=INT
Whether to count unknown (N) characters in the genome as a mismatch (0=no, 1=yes). If --use-mask
is specified, default is no, otherwise yes.
--maxsearch=INT
Maximum number of alignments to find (default 1000). Should be larger than --npaths, which is the
number to report. Keeping this number large will allow for random selection among multiple
alignments. Reducing this number can speed up the program.
--indel-endlength=INT
Minimum length at end required for indel alignments (default 4)
--max-insertions=INT
Maximum number of insertions allowed (default 9)
--max-deletions=INT
Maximum number of deletions allowed (default 15)
-M, --suboptimal-levels=INT
Report suboptimal hits beyond best hit (default 0) All hits with best score plus suboptimal-levels
are reported (Note: Not currently implemented)
-a, --adapter-strip=STRING
Method for removing adapters from reads. Currently allowed values: off, paired. Default is
"off". To turn on, specify "paired", which removes adapters from paired-end reads if they appear
to be present.
-e, --use-mask=STRING
Use genome containing masks (e.g. for non-exons) for scoring preference
-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
--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
-t, --nthreads=INT
Number of worker threads
Splicing options for DNA-Seq
--find-dna-chimeras=INT
Look for distant splicing involving poor splice sites (0=no, 1=yes) If not specified, then default
is to be on unless only known splicing is desired (--use-splicing is specified and --novelsplicing
is off)
Splicing options for RNA-Seq
-N, --novelsplicing=INT
Look for novel splicing (0=no (default), 1=yes)
--splicingdir=STRING
Directory for splicing involving known sites or known introns, as specified by the -s or
--use-splicing flag (default is directory computed from -D and -d flags). Note: can just give
full pathname to the -s flag instead.
-s, --use-splicing=STRING
Look for splicing involving known sites or known introns (in <STRING>.iit), at short or long
distances See README instructions for the distinction between known sites and known introns
--splices-noeval
Do not evaluate splices for probability or intron length, but depend only on sequence alignment
--splices-dump=FILE
Write splice junction information to FILE, in the same format as for STAR plus MaxEnt
probabilities for the two intron positions. Note that in this dump file, the annotation column is
reserved strictly for known introns, and not novel introns that passed some criterion from a first
pass.
--splices-include-knownp
In the file for --splices-dump, include all known introns
--splices-read=FILE
Read allowable splices from FILE, in the same format as for STAR. This is useful if some external
program can evaluate and filter the results from --splices-dump in a first alignment pass, and
then GSNAP can use the filtered splices in a second alignment pass
-w, --localsplicedist=INT
Definition of local novel splicing event (default 200000)
--merge-distant-samechr
Report distant splices on the same chromosome as a single splice, if possible. Will produce a
single SAM line instead of two SAM lines, which is also done for translocations, inversions, and
scramble events
Options for paired-end reads
--pairmax-dna=INT
Max total genomic length for DNA-Seq paired reads, or other reads without splicing (default 2000).
Used if -N or -s is not specified. This value is also used for circular chromosomes when splicing
in linear chromosomes is allowed
--pairmax-rna=INT
Max total genomic length for RNA-Seq paired reads, or other reads that could have a splice
(default 200000). Used if -N or -s is specified. Should probably match the value for -w,
--localsplicedist.
--resolve-inner=INT
Whether to resolve soft-clipping on the insides of paired-end reads (default 1)
--pairexpect=INT
Expected paired-end length, used for resolving soft-clipping on the insides of paired-end reads,
and for pairing DNA-seq reads (default 200)
--pairdev=INT
Allowable deviation from expected paired-end length, used for resolving soft-clipping on the
insides of paired-end reads (default 100).
--pass1-min-support=INT
Threshold read support for learning an intron during pass 1 of --two-pass mode (default 20)
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 customize this behavior with these flags:
-J, --quality-zero-score=INT
FASTQ quality scores are zero at this ASCII value (default is 33 for sanger protocol; for
Illumina, select 64)
-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)
Output options
-n, --npaths=INT
Maximum number of paths to print (default 100).
-Q, --quiet-if-excessive
If more than maximum number of paths are found, then nothing is printed.
-O, --ordered
Print output in same order as input (relevant only if there is more than one worker thread)
--show-refdiff
For GSNAP output in SNP-tolerant alignment, shows all differences relative to the reference genome
as lower case (otherwise, it shows all differences relative to both the reference and alternate
genome)
--clip-overlap
For paired-end reads whose alignments overlap, clip the overlapping region.
--merge-overlap
For paired-end reads whose alignments overlap, merge the two ends into a single end (beta
implementation)
--print-snps
Print detailed information about SNPs in reads (works only if -v also selected) (not fully
implemented yet)
--failsonly
Print only failed alignments, those with no results
--nofails
Exclude printing of failed alignments
--only-concordant
Print only concordant alignments (concordant_uniq, concordant_mult, concordant_circular)
--omit-concordant-uniq
Do not print any concordant_uniq alignments
--omit-concordant-mult
Do not print any concordant_mult alignments
--omit-softclipped
Do not allow any alignments with soft clips
--only-tr-consistent
Print only alignments with consistent transcripts (XX field present, identical if paired-end)
-A, --format=STRING
Another format type, other than default. Currently implemented: sam, m8 (BLAST tabular format)
--split-output=STRING
Basename for multiple-file output, separately for nomapping, halfmapping_uniq, halfmapping_mult,
unpaired_uniq, unpaired_mult, paired_uniq, paired_mult, concordant_uniq, and concordant_mult
results
-o, --output-file=STRING
File name for a single stream of output results.
--failed-input=STRING
Print completely failed alignments as input FASTA or FASTQ format, to the given file, appending .1
or .2, for paired-end data. 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 --failed-input is given, this flag will append output to the existing
files. Otherwise, the default is to create new files.
--order-among-best=STRING
Among alignments tied with the best score, order those alignments in this order. Allowed values:
genomic, random (default)
--output-buffer-size=INT
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
Options for SAM output
--no-sam-headers
Do not print headers beginning with '@'
--add-paired-nomappers
Add nomapper lines as needed to make all paired-end results alternate between first end and second
end
--paired-flag-means-concordant=INT
Whether the paired bit in the SAM flags means concordant only (1) or paired plus concordant (0,
default)
--sam-headers-batch=INT
Print headers only for this batch, as specified by -q
--sam-hardclip-use-S
Use S instead of H for hardclips
--sam-use-0M=INT
If 1 (default), then insert 0M in CIGAR between adjacent indels and introns If 0, do not allow 0M.
Picard disallows 0M, but other tools may require it
--sam-extended-cigar
Use extended CIGAR format (using X and = symbols instead of M, to indicate matches and mismatches,
respectively
--sam-multiple-primaries
Allows multiple alignments to be marked as primary if they have equally good mapping scores
--sam-sparse-secondaries
For secondary alignments (in multiple mappings), uses '*' for SEQ and QUAL fields, to give smaller
file sizes. However, the output will give warnings in Picard to give warnings and may not work
with downstream tools
--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-report-snps
In MD string, when known SNPs are given by the -v flag, prints difference nucleotides when they
differ from reference but match a known alternate allele
--no-soft-clips
Does not allow soft clips at ends. Mismatches will be counted over the entire query
--extend-soft-clips
Extends alignments through soft clipped regions. CIGAR string and coordinates will be revised,
but mismatches and the MD string will reflect the clipped CIGAR
--action-if-cigar-error
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
--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
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
gsnapl 2024-11-20+ds-2 February 2025 GSNAPL(1)