-x <hisat2-idx>

The basename of the index for the reference genome. The basename is the name of any of the index files up to but not including the final .1.ht2 / etc. hisat2 looks for the specified index first in the current directory, then in the directory specified in the HISAT2_INDEXES environment variable.

-1 <m1>

Comma-separated list of files containing mate 1s (filename usually includes _1), e.g. -1 flyA_1.fq,flyB_1.fq. Sequences specified with this option must correspond file-for-file and read-for-read with those specified in <m2>. Reads may be a mix of different lengths. If - is specified, hisat2 will read the mate 1s from the "standard in" or "stdin" filehandle.

-2 <m2>

Comma-separated list of files containing mate 2s (filename usually includes _2), e.g. -2 flyA_2.fq,flyB_2.fq. Sequences specified with this option must correspond file-for-file and read-for-read with those specified in <m1>. Reads may be a mix of different lengths. If - is specified, hisat2 will read the mate 2s from the "standard in" or "stdin" filehandle.

-U <r>

Comma-separated list of files containing unpaired reads to be aligned, e.g. lane1.fq,lane2.fq,lane3.fq,lane4.fq. Reads may be a mix of different lengths. If - is specified, hisat2 gets the reads from the "standard in" or "stdin" filehandle.

--sra-acc <SRA accession number>

Comma-separated list of SRA accession numbers, e.g. --sra-acc SRR353653,SRR353654. Information about read types is available at http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?sp=runinfo&acc=sra-acc&retmode=xml, where sra-acc is SRA accession number. If users run HISAT2 on a computer cluster, it is recommended to disable SRA-related caching (see the instruction at SRA-MANUAL).

-S <hit>

File to write SAM alignments to. By default, alignments are written to the "standard out" or "stdout" filehandle (i.e. the console).

-q

Reads (specified with <m1>, <m2>, <s>) are FASTQ files. FASTQ files usually have extension .fq or .fastq. FASTQ is the default format. See also: --solexa-quals and --int-quals.

--qseq

Reads (specified with <m1>, <m2>, <s>) are QSEQ files. QSEQ files usually end in _qseq.txt. See also: --solexa-quals and --int-quals.

-f

Reads (specified with <m1>, <m2>, <s>) are FASTA files. FASTA files usually have extension .fa, .fasta, .mfa, .fna or similar. FASTA files do not have a way of specifying quality values, so when -f is set, the result is as if --ignore-quals is also set.

-r

Reads (specified with <m1>, <m2>, <s>) are files with one input sequence per line, without any other information (no read names, no qualities). When -r is set, the result is as if --ignore-quals is also set.

-c

The read sequences are given on command line. I.e. <m1>, <m2> and <singles> are comma-separated lists of reads rather than lists of read files. There is no way to specify read names or qualities, so -c also implies --ignore-quals.

-s/--skip <int>

Skip (i.e. do not align) the first <int> reads or pairs in the input.

-u/--qupto <int>

Align the first <int> reads or read pairs from the input (after the -s/--skip reads or pairs have been skipped), then stop. Default: no limit.

-5/--trim5 <int>

Trim <int> bases from 5' (left) end of each read before alignment (default: 0).

-3/--trim3 <int>

Trim <int> bases from 3' (right) end of each read before alignment (default: 0).

--phred33

Input qualities are ASCII chars equal to the Phred quality plus 33. This is also called the "Phred+33" encoding, which is used by the very latest Illumina pipelines.

--phred64

Input qualities are ASCII chars equal to the Phred quality plus 64. This is also called the "Phred+64" encoding.

--solexa-quals

Convert input qualities from Solexa (which can be negative) to Phred (which can't). This scheme was used in older Illumina GA Pipeline versions (prior to 1.3). Default: off.

--int-quals

Quality values are represented in the read input file as space-separated ASCII integers, e.g., 40 40 30 40..., rather than ASCII characters, e.g., II?I.... Integers are treated as being on the Phred quality scale unless --solexa-quals is also specified. Default: off.

--n-ceil <func>

Sets a function governing the maximum number of ambiguous characters (usually Ns and/or .s) allowed in a read as a function of read length. For instance, specifying -L,0,0.15 sets the N-ceiling function f to f(x) = 0 + 0.15 * x, where x is the read length. See also: [setting function options]. Reads exceeding this ceiling are filtered out. Default: L,0,0.15.

--ignore-quals

When calculating a mismatch penalty, always consider the quality value at the mismatched position to be the highest possible, regardless of the actual value. I.e. input is treated as though all quality values are high. This is also the default behavior when the input doesn't specify quality values (e.g. in -f, -r, or -c modes).

--nofw/--norc

If --nofw is specified, hisat2 will not attempt to align unpaired reads to the forward (Watson) reference strand. If --norc is specified, hisat2 will not attempt to align unpaired reads against the reverse-complement (Crick) reference strand. In paired-end mode, --nofw and --norc pertain to the fragments; i.e. specifying --nofw causes hisat2 to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand. Default: both strands enabled.

--mp MX,MN

Sets the maximum (MX) and minimum (MN) mismatch penalties, both integers. A number less than or equal to MX and greater than or equal to MN is subtracted from the alignment score for each position where a read character aligns to a reference character, the characters do not match, and neither is an N. If --ignore-quals is specified, the number subtracted quals MX. Otherwise, the number subtracted is MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) ) where Q is the Phred quality value. Default: MX = 6, MN = 2.

--sp MX,MN

Sets the maximum (MX) and minimum (MN) penalties for soft-clipping per base, both integers. A number less than or equal to MX and greater than or equal to MN is subtracted from the alignment score for each position. The number subtracted is MN + floor( (MX-MN)(MIN(Q, 40.0)/40.0) ) where Q is the Phred quality value. Default: MX = 2, MN = 1.

--no-softclip

Disallow soft-clipping.

--np <int>

Sets penalty for positions where the read, reference, or both, contain an ambiguous character such as N. Default: 1.

--rdg <int1>,<int2>

Sets the read gap open (<int1>) and extend (<int2>) penalties. A read gap of length N gets a penalty of <int1> + N * <int2>. Default: 5, 3.

--rfg <int1>,<int2>

Sets the reference gap open (<int1>) and extend (<int2>) penalties. A reference gap of length N gets a penalty of <int1> + N * <int2>. Default: 5, 3.

--score-min <func>

Sets a function governing the minimum alignment score needed for an alignment to be considered "valid" (i.e. good enough to report). This is a function of read length. For instance, specifying L,0,-0.6 sets the minimum-score function f to f(x) = 0 + -0.6 * x, where x is the read length. See also: [setting function options]. The default is L,0,-0.2.

--pen-cansplice <int>

Sets the penalty for each pair of canonical splice sites (e.g. GT/AG). Default: 0.

--pen-noncansplice <int>

Sets the penalty for each pair of non-canonical splice sites (e.g. non-GT/AG). Default: 12.

--pen-canintronlen <func>

Sets the penalty for long introns with canonical splice sites so that alignments with shorter introns are preferred to those with longer ones. Default: G,-8,1

--pen-noncanintronlen <func>

Sets the penalty for long introns with noncanonical splice sites so that alignments with shorter introns are preferred to those with longer ones. Default: G,-8,1

--min-intronlen <int>

Sets minimum intron length. Default: 20

--max-intronlen <int>

Sets maximum intron length. Default: 500000

--known-splicesite-infile <path>

With this mode, you can provide a list of known splice sites, which HISAT2 makes use of to align reads with small anchors.
You can create such a list using python hisat2_extract_splice_sites.py genes.gtf > splicesites.txt, where hisat2_extract_splice_sites.py is included in the HISAT2 package, genes.gtf is a gene annotation file, and splicesites.txt is a list of splice sites with which you provide HISAT2 in this mode. Note that it is better to use indexes built using annotated transcripts (such as genome_tran or genome_snp_tran), which works better than using this option. It has no effect to provide splice sites that are already included in the indexes.

--novel-splicesite-outfile <path>

In this mode, HISAT2 reports a list of splice sites in the file :
chromosome name <tab> genomic position of the flanking base on the left side of an intron <tab> genomic position of the flanking base on the right <tab> strand (+, -, and .) '.' indicates an unknown strand for non-canonical splice sites.

--novel-splicesite-infile <path>

With this mode, you can provide a list of novel splice sites that were generated from the above option "--novel-splicesite-outfile".

--no-temp-splicesite

HISAT2, by default, makes use of splice sites found by earlier reads to align later reads in the same run, in particular, reads with small anchors (<= 15 bp).
The option disables this default alignment strategy.

--no-spliced-alignment

Disable spliced alignment.

--rna-strandness <string>

Specify strand-specific information: the default is unstranded.
For single-end reads, use F or R. 'F' means a read corresponds to a transcript. 'R' means a read corresponds to the reverse complemented counterpart of a transcript. For paired-end reads, use either FR or RF.
With this option being used, every read alignment will have an XS attribute tag: '+' means a read belongs to a transcript on '+' strand of genome. '-' means a read belongs to a transcript on '-' strand of genome.

--tmo/--transcriptome-mapping-only

Report only those alignments within known transcripts.

--dta/--downstream-transcriptome-assembly

Report alignments tailored for transcript assemblers including StringTie. With this option, HISAT2 requires longer anchor lengths for de novo discovery of splice sites. This leads to fewer alignments with short-anchors, which helps transcript assemblers improve significantly in computation and memory usage.

--dta-cufflinks

Report alignments tailored specifically for Cufflinks. In addition to what HISAT2 does with the above option (--dta), With this option, HISAT2 looks for novel splice sites with three signals (GT/AG, GC/AG, AT/AC), but all user-provided splice sites are used irrespective of their signals. HISAT2 produces an optional field, XS:A:[+-], for every spliced alignment.

--no-templatelen-adjustment

Disables template length adjustment for RNA-seq reads.

-k <int>

It searches for at most <int> distinct, primary alignments for each read. Primary alignments mean alignments whose alignment score is equal or higher than any other alignments. The search terminates when it can't find more distinct valid alignments, or when it finds <int>, whichever happens first. The alignment score for a paired-end alignment equals the sum of the alignment scores of the individual mates. Each reported read or pair alignment beyond the first has the SAM 'secondary' bit (which equals 256) set in its FLAGS field. For reads that have more than <int> distinct, valid alignments, hisat2 does not guarantee that the <int> alignments reported are the best possible in terms of alignment score. Default: 5 (HFM) or 10 (HGFM)

Note: HISAT2 is not designed with large values for -k in mind, and when aligning reads to long, repetitive genomes large -k can be very, very slow.

--max-seeds <int>

HISAT2, like other aligners, uses seed-and-extend approaches. HISAT2 tries to extend seeds to full-length alignments. In HISAT2, --max-seeds is used to control the maximum number of seeds that will be extended. HISAT2 extends up to these many seeds and skips the rest of the seeds. Large values for --max-seeds may improve alignment sensitivity, but HISAT2 is not designed with large values for --max-seeds in mind, and when aligning reads to long, repetitive genomes large --max-seeds can be very, very slow. The default value is the maximum of 5 and the value that comes with-k.

--secondary

Report secondary alignments.

-I/--minins <int>

The minimum fragment length for valid paired-end alignments.This option is valid only with --no-spliced-alignment. E.g. if -I 60 is specified and a paired-end alignment consists of two 20-bp alignments in the appropriate orientation with a 20-bp gap between them, that alignment is considered valid (as long as -X is also satisfied). A 19-bp gap would not be valid in that case. If trimming options -3 or -5 are also used, the -I constraint is applied with respect to the untrimmed mates.

The larger the difference between -I and -X, the slower HISAT2 will run. This is because larger differences between -I and -X require that HISAT2 scan a larger window to determine if a concordant alignment exists. For typical fragment length ranges (200 to 400 nucleotides), HISAT2 is very efficient.

Default: 0 (essentially imposing no minimum)

-X/--maxins <int>

The maximum fragment length for valid paired-end alignments. This option is valid only with --no-spliced-alignment. E.g. if -X 100 is specified and a paired-end alignment consists of two 20-bp alignments in the proper orientation with a 60-bp gap between them, that alignment is considered valid (as long as -I is also satisfied). A 61-bp gap would not be valid in that case. If trimming options -3 or -5 are also used, the -X constraint is applied with respect to the untrimmed mates, not the trimmed mates.

The larger the difference between -I and -X, the slower HISAT2 will run. This is because larger differences between -I and -X require that HISAT2 scan a larger window to determine if a concordant alignment exists. For typical fragment length ranges (200 to 400 nucleotides), HISAT2 is very efficient.

Default: 500.

--fr/--rf/--ff

The upstream/downstream mate orientations for a valid paired-end alignment against the forward reference strand. E.g., if --fr is specified and there is a candidate paired-end alignment where mate 1 appears upstream of the reverse complement of mate 2 and the fragment length constraints (-I and -X) are met, that alignment is valid. Also, if mate 2 appears upstream of the reverse complement of mate 1 and all other constraints are met, that too is valid. --rf likewise requires that an upstream mate1 be reverse-complemented and a downstream mate2 be forward-oriented. --ff requires both an upstream mate 1 and a downstream mate 2 to be forward-oriented. Default: --fr (appropriate for Illumina's Paired-end Sequencing Assay).

--no-mixed

By default, when hisat2 cannot find a concordant or discordant alignment for a pair, it then tries to find alignments for the individual mates. This option disables that behavior.

--no-discordant

By default, hisat2 looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (--fr/--rf/--ff, -I, -X). This option disables that behavior.

-t/--time

Print the wall-clock time required to load the index files and align the reads. This is printed to the "standard error" ("stderr") filehandle. Default: off.

--un <path>
--un-gz <path>
--un-bz2 <path>

Write unpaired reads that fail to align to file at <path>. These reads correspond to the SAM records with the FLAGS 0x4 bit set and neither the 0x40 nor 0x80 bits set. If --un-gz is specified, output will be gzip compressed. If --un-bz2 is specified, output will be bzip2 compressed. Reads written in this way will appear exactly as they did in the input file, without any modification (same sequence, same name, same quality string, same quality encoding). Reads will not necessarily appear in the same order as they did in the input.

--al <path>
--al-gz <path>
--al-bz2 <path>

Write unpaired reads that align at least once to file at <path>. These reads correspond to the SAM records with the FLAGS 0x4, 0x40, and 0x80 bits unset. If --al-gz is specified, output will be gzip compressed. If --al-bz2 is specified, output will be bzip2 compressed. Reads written in this way will appear exactly as they did in the input file, without any modification (same sequence, same name, same quality string, same quality encoding). Reads will not necessarily appear in the same order as they did in the input.

--un-conc <path>
--un-conc-gz <path>
--un-conc-bz2 <path>

Write paired-end reads that fail to align concordantly to file(s) at <path>. These reads correspond to the SAM records with the FLAGS 0x4 bit set and either the 0x40 or 0x80 bit set (depending on whether it's mate #1 or #2). .1 and .2 strings are added to the filename to distinguish which file contains mate #1 and mate #2. If a percent symbol, %, is used in <path>, the percent symbol is replaced with 1 or 2 to make the per-mate filenames. Otherwise, .1 or .2 are added before the final dot in <path> to make the per-mate filenames. Reads written in this way will appear exactly as they did in the input files, without any modification (same sequence, same name, same quality string, same quality encoding). Reads will not necessarily appear in the same order as they did in the inputs.

--al-conc <path>
--al-conc-gz <path>
--al-conc-bz2 <path>

Write paired-end reads that align concordantly at least once to file(s) at <path>. These reads correspond to the SAM records with the FLAGS 0x4 bit unset and either the 0x40 or 0x80 bit set (depending on whether it's mate #1 or #2). .1 and .2 strings are added to the filename to distinguish which file contains mate #1 and mate #2. If a percent symbol, %, is used in <path>, the percent symbol is replaced with 1 or 2 to make the per-mate filenames. Otherwise, .1 or .2 are added before the final dot in <path> to make the per-mate filenames. Reads written in this way will appear exactly as they did in the input files, without any modification (same sequence, same name, same quality string, same quality encoding). Reads will not necessarily appear in the same order as they did in the inputs.

--quiet

Print nothing besides alignments and serious errors.

--summary-file

Print alignment summary to this file.

--new-summary

Print alignment summary in a new style, which is more machine-friendly.

--met-file <path>

Write hisat2 metrics to file <path>. Having alignment metric can be useful for debugging certain problems, especially performance issues. See also: --met. Default: metrics disabled.

--met-stderr

Write hisat2 metrics to the "standard error" ("stderr") filehandle. This is not mutually exclusive with --met-file. Having alignment metric can be useful for debugging certain problems, especially performance issues. See also: --met. Default: metrics disabled.

--met <int>

Write a new hisat2 metrics record every <int> seconds. Only matters if either --met-stderr or --met-file are specified. Default: 1.

--no-unal

Suppress SAM records for reads that failed to align.

--no-hd

Suppress SAM header lines (starting with @).

--no-sq

Suppress @SQ SAM header lines.

--rg-id <text>

Set the read group ID to <text>. This causes the SAM @RG header line to be printed, with <text> as the value associated with the ID: tag. It also causes the RG:Z: extra field to be attached to each SAM output record, with value set to <text>.

--rg <text>

Add <text> (usually of the form TAG:VAL, e.g. SM:Pool1) as a field on the @RG header line. Note: in order for the @RG line to appear, --rg-id must also be specified. This is because the ID tag is required by the SAM Spec. Specify --rg multiple times to set multiple fields. See the SAM Spec for details about what fields are legal.

--remove-chrname

Remove 'chr' from reference names in alignment (e.g., chr18 to 18)

--add-chrname

Add 'chr' to reference names in alignment (e.g., 18 to chr18)

--omit-sec-seq

When printing secondary alignments, HISAT2 by default will write out the SEQ and QUAL strings. Specifying this option causes HISAT2 to print an asterisk in those fields instead.

-o/--offrate <int>

Override the offrate of the index with <int>. If <int> is greater than the offrate used to build the index, then some row markings are discarded when the index is read into memory. This reduces the memory footprint of the aligner but requires more time to calculate text offsets. <int> must be greater than the value used to build the index.

-p/--threads NTHREADS

Launch NTHREADS parallel search threads (default: 1). Threads will run on separate processors/cores and synchronize when parsing reads and outputting alignments. Searching for alignments is highly parallel, and speedup is close to linear. Increasing -p increases HISAT2's memory footprint. E.g. when aligning to a human genome index, increasing -p from 1 to 8 increases the memory footprint by a few hundred megabytes. This option is only available if bowtie is linked with the pthreads library (i.e. if BOWTIE_PTHREADS=0 is not specified at build time).

--reorder

Guarantees that output SAM records are printed in an order corresponding to the order of the reads in the original input file, even when -p is set greater than 1. Specifying --reorder and setting -p greater than 1 causes HISAT2 to run somewhat slower and use somewhat more memory then if --reorder were not specified. Has no effect if -p is set to 1, since output order will naturally correspond to input order in that case.

--mm

Use memory-mapped I/O to load the index, rather than typical file I/O. Memory-mapping allows many concurrent bowtie processes on the same computer to share the same memory image of the index (i.e. you pay the memory overhead just once). This facilitates memory-efficient parallelization of bowtie in situations where using -p is not possible or not preferable.

--qc-filter

Filter out reads for which the QSEQ filter field is non-zero. Only has an effect when read format is --qseq. Default: off.

--seed <int>

Use <int> as the seed for pseudo-random number generator. Default: 0.

--non-deterministic

Normally, HISAT2 re-initializes its pseudo-random generator for each read. It seeds the generator with a number derived from (a) the read name, (b) the nucleotide sequence, (c) the quality sequence, (d) the value of the --seed option. This means that if two reads are identical (same name, same nucleotides, same qualities) HISAT2 will find and report the same alignment(s) for both, even if there was ambiguity. When --non-deterministic is specified, HISAT2 re-initializes its pseudo-random generator for each read using the current time. This means that HISAT2 will not necessarily report the same alignment for two identical reads. This is counter-intuitive for some users, but might be more appropriate in situations where the input consists of many identical reads.

--version

Print version information and quit.

-h/--help

Print usage information and quit.

<reference_in>

A comma-separated list of FASTA files containing the reference sequences to be aligned to, or, if -c is specified, the sequences themselves. E.g., <reference_in> might be chr1.fa,chr2.fa,chrX.fa,chrY.fa, or, if -c is specified, this might be GGTCATCCT,ACGGGTCGT,CCGTTCTATGCGGCTTA.

<ht2_base>

The basename of the index files to write. By default, hisat2-build writes files named NAME.1.ht2, NAME.2.ht2, NAME.3.ht2, NAME.4.ht2, NAME.5.ht2, NAME.6.ht2, NAME.7.ht2, and NAME.8.ht2 where NAME is <ht2_base>.

-f

The reference input files (specified as <reference_in>) are FASTA files (usually having extension .fa, .mfa, .fna or similar).

-c

The reference sequences are given on the command line. I.e. <reference_in> is a comma-separated list of sequences rather than a list of FASTA files.

--large-index

Force hisat2-build to build a large index, even if the reference is less than ~ 4 billion nucleotides long.

-a/--noauto

Disable the default behavior whereby hisat2-build automatically selects values for the --bmax, --dcv and [--packed] parameters according to available memory. Instead, user may specify values for those parameters. If memory is exhausted during indexing, an error message will be printed; it is up to the user to try new parameters.

--bmax <int>

The maximum number of suffixes allowed in a block. Allowing more suffixes per block makes indexing faster, but increases peak memory usage. Setting this option overrides any previous setting for --bmax, or --bmaxdivn. Default (in terms of the --bmaxdivn parameter) is --bmaxdivn 4. This is configured automatically by default; use -a/--noauto to configure manually.

--bmaxdivn <int>

The maximum number of suffixes allowed in a block, expressed as a fraction of the length of the reference. Setting this option overrides any previous setting for --bmax, or --bmaxdivn. Default: --bmaxdivn 4. This is configured automatically by default; use -a/--noauto to configure manually.

--dcv <int>

Use <int> as the period for the difference-cover sample. A larger period yields less memory overhead, but may make suffix sorting slower, especially if repeats are present. Must be a power of 2 no greater than 4096. Default: 1024. This is configured automatically by default; use -a/--noauto to configure manually.

--nodc

Disable use of the difference-cover sample. Suffix sorting becomes quadratic-time in the worst case (where the worst case is an extremely repetitive reference). Default: off.

-r/--noref

Do not build the NAME.3.ht2 and NAME.4.ht2 portions of the index, which contain a bitpacked version of the reference sequences and are used for paired-end alignment.

-3/--justref

Build only the NAME.3.ht2 and NAME.4.ht2 portions of the index, which contain a bitpacked version of the reference sequences and are used for paired-end alignment.

-o/--offrate <int>

To map alignments back to positions on the reference sequences, it's necessary to annotate ("mark") some or all of the Burrows-Wheeler rows with their corresponding location on the genome. -o/--offrate governs how many rows get marked: the indexer will mark every 2^<int> rows. Marking more rows makes reference-position lookups faster, but requires more memory to hold the annotations at runtime. The default is 4 (every 16th row is marked; for human genome, annotations occupy about 680 megabytes).

-t/--ftabchars <int>

The ftab is the lookup table used to calculate an initial Burrows-Wheeler range with respect to the first <int> characters of the query. A larger <int> yields a larger lookup table but faster query times. The ftab has size 4^(<int>+1) bytes. The default setting is 10 (ftab is 4MB).

--localoffrate <int>

This option governs how many rows get marked in a local index: the indexer will mark every 2^<int> rows. Marking more rows makes reference-position lookups faster, but requires more memory to hold the annotations at runtime. The default is 3 (every 8th row is marked, this occupies about 16KB per local index).

--localftabchars <int>

The local ftab is the lookup table in a local index. The default setting is 6 (ftab is 8KB per local index).

-p <int>

Launch NTHREADS parallel build threads (default: 1).

--snp <path>

Provide a list of SNPs (in the HISAT2's own format) as follows (five columns).

SNP ID <tab> snp type (single, deletion, or insertion) <tab> chromosome name <tab> zero-offset based genomic position of a SNP <tab> alternative base (single), the length of SNP (deletion), or insertion sequence (insertion)

For example, rs58784443 single 13 18447947 T

Use hisat2_extract_snps_haplotypes_UCSC.py (in the HISAT2 package) to extract SNPs and haplotypes from a dbSNP file (e.g. http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/snp144Common.txt.gz). or hisat2_extract_snps_haplotypes_VCF.py to extract SNPs and haplotypes from a VCF file (e.g. ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/supporting/GRCh38_positions/ALL.chr22.phase3_shapeit2_mvncall_integrated_v3plus_nounphased.rsID.genotypes.GRCh38_dbSNP_no_SVs.vcf.gz).

--haplotype <path>

Provide a list of haplotypes (in the HISAT2's own format) as follows (five columns).

Haplotype ID <tab> chromosome name <tab> zero-offset based left coordinate of haplotype <tab> zero-offset based right coordinate of haplotype <tab> a comma separated list of SNP ids in the haplotype

For example, ht35 13 18446877 18446945 rs12381094,rs12381056,rs192016659,rs538569910

See the above option, --snp, about how to extract haplotypes. This option is not required, but haplotype information can keep the index construction from exploding and reduce the index size substantially.

--ss <path>

Note this option should be used with the following --exon option. Provide a list of splice sites (in the HISAT2's own format) as follows (four columns).

chromosome name <tab> zero-offset based genomic position of the flanking base on the left side of an intron <tab> zero-offset based genomic position of the flanking base on the right <tab> strand

Use hisat2_extract_splice_sites.py (in the HISAT2 package) to extract splice sites from a GTF file.

--exon <path>

Note this option should be used with the above --ss option. Provide a list of exons (in the HISAT2's own format) as follows (three columns).

chromosome name <tab> zero-offset based left genomic position of an exon <tab> zero-offset based right genomic position of an exon

Use hisat2_extract_exons.py (in the HISAT2 package) to extract exons from a GTF file.

--seed <int>

Use <int> as the seed for pseudo-random number generator.

--cutoff <int>

Index only the first <int> bases of the reference sequences (cumulative across sequences) and ignore the rest.

-q/--quiet

hisat2-build is verbose by default. With this option hisat2-build will print only error messages.

-h/--help

Print usage information and quit.

--version

Print version information and quit.

<ht2_base>

The basename of the index to be inspected. The basename is name of any of the index files but with the .X.ht2 suffix omitted. hisat2-inspect first looks in the current directory for the index files, then in the directory specified in the HISAT2_INDEXES environment variable.

-a/--across <int>

When printing FASTA output, output a newline character every <int> bases (default: 60).

-n/--names

Print reference sequence names, one per line, and quit.

-s/--summary

Print a summary that includes information about index settings, as well as the names and lengths of the input sequences. The summary has this format:

Colorspace  <0 or 1>
SA-Sample   1 in <sample>
FTab-Chars  <chars>
Sequence-1  <name>  <len>
Sequence-2  <name>  <len>
...
Sequence-N  <name>  <len>

Fields are separated by tabs. Colorspace is always set to 0 for HISAT2.

--snp

Print SNPs, and quit.

--ss

Print splice sites, and quit.

--ss-all

Print splice sites including those not in the global index, and quit.

--exon

Print exons, and quit.

-v/--verbose

Print verbose output (for debugging).

--version

Print version information and quit.

-h/--help

Print usage information and quit.