Provided by: gmap_2021-12-17+ds-1_amd64 
NAME
gsnap - Genomic 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
--use-localdb=INT
Whether to use the local hash tables, 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
--use-transcriptome-only
Use only the transcriptome index and not the genome index
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
-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 = 2)
Mode Hash offsets Hash positions Genome Local hash offsets Local hash
positions
0 allocate mmap mmap allocate mmap
1 allocate mmap & preload mmap allocate mmap & preload
2 allocate mmap & preload mmap & preload allocate mmap & preload
3 allocate allocate mmap & preload allocate allocate
(default)
4 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
--max-ref-mismatches=FLOAT
If GSNAP is run under SNP-tolerant or masked genome mode, then the --max-mismatches parameter
above is for mismatches against reference and SNPs, or against the unmasked genome, respectively.
The --max-ref-mismatches parameter is against mismatches against the reference genome or masked
genome.
--min-coverage=FLOAT
Minimum coverage required for an alignment. If specified between 0.0 and 1.0, then treated as a
fraction of each read length. Otherwise, treated as an integral number of base pairs. Default
value is 0.5.
--filter-within-trims=INT
Whether to count mismatches in trimmed part of alignment (1, yes) or mismatches to the ends of the
read (0, no), when applying the --max-mismatches and --max-ref-mismatches parameters. Default for
RNA-Seq is 1 (yes) so we can allow for reads that align past the ends of an exon. Default for
DNA-Seq is 0 (no).
For RNA-Seq, trimmed ends should be ignored, because trimming
is performed at probable splice sites, to allow for reads that align past the ends of an exon.
--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.
-i, --indel-penalty=INT
Penalty for an indel (default 2). Counts against mismatches allowed. To find indels, make
indel-penalty less than or equal to max-mismatches. A value < 2 can lead to false positives at
read ends
--indel-endlength=INT
Minimum length at end required for indel alignments (default 4)
-y, --max-middle-insertions=FLOAT
Maximum number of middle insertions allowed (default is 0.2) If specified between 0.0 and 1.0,
then treated as a fraction of each read length. Otherwise, treated as an integral number of base
pairs
-z, --max-middle-deletions=FLOAT
Maximum number of middle deletions allowed (default 0.2) If specified between 0.0 and 1.0, then
treated as a fraction of each read length. Otherwise, treated as an integral number of base pairs
-Y, --max-end-insertions=INT
Maximum number of end insertions allowed (default 3)
-Z, --max-end-deletions=INT
Maximum number of end deletions allowed (default 3)
-M, --suboptimal-levels=INT
Report suboptimal hits beyond best hit (default 0) All hits with best score plus suboptimal-levels
are reported
-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.
--trim-indel-score=INT
Score to use for indels when trimming at ends. To turn off trimming, specify 0. Default is -2
for both RNA-Seq and DNA-Seq. Warning: Turning trimming off in RNA-Seq can give false positive
indels at the ends of reads
-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
--max-anchors=INT
Controls number of candidate segments returned by the complete set algorithm Default is 10. Can
be increased to higher values to solve alignments with evenly spaced mismatches at close
distances. However, higher values will cause GSNAP to run more slowly. A value of 1000, for
example, slows down the program by a factor of 10 or so. Therefore, change this value only if
absolutely necessary.
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
--ambig-splice-noclip
For ambiguous known splicing at ends of the read, do not clip at the splice site, but extend
instead into the intron. This flag makes sense only if you provide the --use-splicing flag, and
you are trying to eliminate all soft clipping with --trim-mismatch-score=0
-w, --localsplicedist=INT
Definition of local novel splicing event (default 200000)
--novelend-splicedist=INT
Distance to look for novel splices at the ends of reads (default 80000)
--local-splice-penalty=INT
Penalty for a local splice (default 0). Counts against mismatches allowed
--fusion-sensitivity=INT
Sensitivity for finding fusions
--distant-splice-penalty=INT
Penalty for a distant splice (default 1). A distant splice is one where the intron length exceeds
the value of -w, or --localsplicedist, or is an inversion, scramble, or translocation between two
different chromosomes Counts against mismatches allowed
--distant-splice-endlength=INT
Minimum length at end required for distant spliced alignments (default 20, min allowed is the
value of -k, or kmer size)
--shortend-splice-endlength=INT
Minimum length at end required for short-end spliced alignments (default 2, but unless known
splice sites are provided with the -s flag, GSNAP may still need the end length to be the value of
-k, or kmer size to find a given splice
--distant-splice-identity=FLOAT
Minimum identity at end required for distant spliced alignments (default 0.95)
--antistranded-penalty=INT
(Not currently implemented, since it leads to poor results) Penalty for antistranded splicing when
using stranded RNA-Seq protocols. A positive value, such as 1, expects antisense on the first
read and sense on the second read. Default is 0, which treats sense and antisense equally well
--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.
--pairexpect=INT
Expected paired-end length, used for calling splices in medial part of paired-end reads (default
500). Was turned off in previous versions, but reinstated.
--pairdev=INT
Allowable deviation from expected paired-end length, used for calling splices in medial part of
paired-end reads (default 100). Was turned off in previous versions, but reinstated.
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
-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
Insert 0M in CIGAR between adjacent insertions, deletions, and introns Picard disallows 0M, 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-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
--extend-soft-clips
Extends alignments through soft clipped regions. CIGAR string and coordinates will be revised,
but currently 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
gsnap 2021-12-17+ds-1 January 2022 GSNAP(1)