gsnap (1)

NAME

gsnap - Genomic Short-read Nucleotide Alignment Program

SYNOPSIS

gsnap -dDB [OPTION]... [QUERY]...

DESCRIPTION

Align the sequences QUERY to the reference DB. With no QUERY, read standard input.

OPTIONS

Input options

-D, --dir=directory: Genome directory
-d, --db=STRING: Genome database
-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
-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)
--barcode-length=INT: Amount of barcode to remove from start of read (default 0)
-o, --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)
--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
--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).

Computation options

Note: GSNAP has an ultrafast algorithm for calculating mismatches up to and including ((readlength+2)/kmer - 2) ("ultrafast mismatches"). The program will run fastest if max-mismatches (plus suboptimal-levels) is within that value. Also, indels, especially end indels, take longer to compute, although the algorithm is still designed to be fast.

-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)
-m, --max-mismatches=FLOAT: Maximum number of mismatches allowed (if not specified, then defaults to the ultrafast level of ((readlength+2)/kmer - 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 mismatches (including indel and splicing penalties) For RNA-Seq, you may need to increase this value slightly to align reads extending 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 (default))
--terminal-threshold=INT: Threshold for searching for a terminal alignment (from one end of the read to the best possible position at the other end) (default 2). For example, if this value is 2, then if GSNAP finds an exact or 1-mismatch alignment, it will not try to find a terminal alignment. Note that this default value may not be low enough if you want to obtain terminal alignments for very short reads, although such reads probably don't have enough specificity for terminal alignments anyway. To turn off terminal alignments, set this to a high value, greater than the value for --max-mismatches.
-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=INT: Maximum number of middle insertions allowed (default 9)
-z, --max-middle-deletions=INT: Maximum number of middle deletions allowed (default 30)
-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 6)
-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 "paired", which removes adapters from paired-end reads if a concordant or paired alignment cannot be found from the original read. To turn off, use the value "off".
--trim-mismatch-score=INT: Score to use for mismatches when trimming at ends (default is -3; to turn off trimming, specify 0). Warning: turning trimming off will give false positive mismatches at the ends of reads
--trim-indel-score=INT: Score to use for indels when trimming at ends (default is -4; to turn off trimming, specify 0). Warning: turning trimming off will give false positive indels at the ends of reads
-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, or atoi-nonstranded. Non-standard modes requires you to have previously run the cmetindex or atoiindex programs on the genome
--tallydir=STRING: Directory for tally IIT file to resolve concordant multiple results (default is location of genome index files specified using -D and -d). Note: can just give full path name to --use-tally instead.
--use-tally=STRING: Use this tally IIT file to resolve concordant multiple results
--runlengthdir=STRING: Directory for runlength IIT file to resolve concordant multiple results (default is location of genome index files specified using -D and -d). Note: can just give full path name to --use-runlength instead.
--use-runlength=STRING: Use this runlength IIT file to resolve concordant multiple results
-t, --nthreads=INT: Number of worker threads

Options for GMAP alignment within GSNAP

--gmap-mode=STRING: Cases to use GMAP for complex alignments containing multiple splices or indels. Allowed values: none, pairsearch, indel_knownsplice, terminal, improve (or multiple values, separated by commas). Default: all on, i.e., pairsearch,indel_knownsplice,terminal,improve
--trigger-score-for-gmap=INT: Try GMAP pairsearch on nearby genomic regions if best score (the total of both ends if paired-end) exceeds this value (default 5)
--max-gmap-pairsearch=INT: Perform GMAP pairsearch on nearby genomic regions up to this many many candidate ends (default 10). Requires pairsearch in --gmap-mode
--max-gmap-terminal=INT: Perform GMAP terminal on nearby genomic regions up to this many candidate ends (default 5). Requires terminal in --gmap-mode
--max-gmap-improvement=INT: Perform GMAP improvement on nearby genomic regions up to this many candidate ends (default 5). Requires improve in --gmap-mode
--microexon-spliceprob=FLOAT: Allow microexons only if one of the splice site probabilities is greater than this value (default 0.90)

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)
-e, --local-splice-penalty=INT: Penalty for a local splice (default 0). Counts against mismatches allowed
-E, --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
-K, --distant-splice-endlength=INT: Minimum length at end required for distant spliced alignments (default 16, min allowed is the value of -k, or kmer size)
-l, --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) 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 1000). Used if -N or -s is not specified.
--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 200)
--pairdev=INT: Allowable deviation from expected paired-end length, used for calling splices in medial part of paired-end reads (default 25)

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.
--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
--fails-as-input: Print completely failed alignments as input FASTA or FASTQ format
-A, --format=STRING: Another format type, other than default. Currently implemented: sam Also allowed, but not installed at compile-time: goby (To install, need to re-compile with appropriate options)
--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

Options for SAM output

--no-sam-headers: Do not print headers beginning with '@'
--sam-headers-batch=INT: Print headers only for this batch, as specified by -q
--sam-use-0M: Insert 0M in CIGAR between adjacent insertions and deletions Required by Picard, but can cause errors in other tools
--sam-multiple-primaries: Allows multiple alignments to be marked as primary if they have equally good mapping scores
--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

--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>.