.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH YARA_MAPPER "1" "June 2017" "yara_mapper 2.3.1+dfsg-4" "User Commands"
.SH NAME
yara_mapper \- Yara Mapper
.PP
SYNOPSIS
.IP
yara_mapper [OPTIONS] <REFERENCE INDEX PREFIX> <SE\-READS FILE>
yara_mapper [OPTIONS] <REFERENCE INDEX PREFIX> <PE\-READS FILE 1> <PE\-READS
FILE 2>
.PP
DESCRIPTION
.IP
Yara \- Yet Another Read Aligner.
.IP
See http://www.seqan.de/projects/yara for more information.
.IP
(c) Copyright 2011\-2014 by Enrico Siragusa.
.IP
(c) Copyright 2013 by NVIDIA Corporation.
.PP
REQUIRED ARGUMENTS
.IP
REFERENCE_INDEX_PREFIX INPUT_PREFIX
.IP
An indexed reference genome.
.IP
READS_FILE List of INPUT_FILE's
.IP
Either one single\-end or two paired\-end / mate\-pair read files.
Valid filetypes are: .sam[.*], .raw[.*], .gbk[.*], .frn[.*],
\&.fq[.*], .fna[.*], .ffn[.*], .fastq[.*], .fasta[.*], .faa[.*],
\&.fa[.*], .embl[.*], and .bam, where * is any of the following
extensions: gz, bz2, and bgzf for transparent (de)compression.
.PP
OPTIONS
.HP
\fB\-h\fR, \fB\-\-help\fR
.IP
Display the help message.
.HP
\fB\-\-version\-check\fR BOOL
.IP
Turn this option off to disable version update notifications of the
application. One of 1, ON, TRUE, T, YES, 0, OFF, FALSE, F, and NO.
Default: 1.
.HP
\fB\-\-version\fR
.IP
Display version information.
.HP
\fB\-v\fR, \fB\-\-verbose\fR
.IP
Displays global statistics.
.HP
\fB\-vv\fR, \fB\-\-very\-verbose\fR
.IP
Displays extensive statistics for each batch of reads.
.IP
Output Options:
.HP
\fB\-o\fR, \fB\-\-output\-file\fR OUTPUT_FILE
.IP
Specify an output file. Default: write the file to standard output.
Valid filetypes are: .sam[.*] and .bam, where * is any of the
following extensions: gz, bz2, and bgzf for transparent
(de)compression.
.HP
\fB\-f\fR, \fB\-\-output\-format\fR STRING
.IP
Specify an output format. Note: when specifying the option
\fB\-\-output\-file\fR, the output format is taken from the filename
extension. One of bam, sam, sam.bgzf, sam.gz, and sam.bz2. Default:
sam.
.HP
\fB\-rg\fR, \fB\-\-read\-group\fR STRING
.IP
Specify a read group for all records in the SAM/BAM file. Default:
none.
.HP
\fB\-sa\fR, \fB\-\-secondary\-alignments\fR STRING
.IP
Specify whether to output secondary alignments in the XA tag of the
primary alignment, as separate secondary records, or to omit them.
One of tag, record, and omit. Default: tag.
.HP
\fB\-ra\fR, \fB\-\-rabema\-alignments\fR
.IP
Output alignments compatible with the Read Alignment BEnchMArk
(RABEMA).
.IP
Mapping Options:
.HP
\fB\-e\fR, \fB\-\-error\-rate\fR INTEGER
.IP
Consider alignments within this percentual number of errors.
Increase this threshold to increase the number of mapped reads.
Decrease this threshold to decrease the runtime. In range [0..10].
Default: 5.
.HP
\fB\-s\fR, \fB\-\-strata\-rate\fR INTEGER
.IP
Consider suboptimal alignments within this percentual number of
errors from the optimal alignment. Increase this threshold to
increase the number of alternative alignments at the expense of
runtime. In range [0..10]. Default: 0.
.HP
\fB\-y\fR, \fB\-\-sensitivity\fR STRING
.IP
Sensitivity with respect to edit distance. Full sensitivity
guarantees to find all considered alignments but increases runtime,
low sensitivity decreases runtime by breaking such guarantee. One of
low, high, and full. Default: high.
.IP
Paired\-End Mapping Options:
.HP
\fB\-ll\fR, \fB\-\-library\-length\fR INTEGER
.IP
Expected library length. Default: autodetected. In range [1..inf].
.HP
\fB\-ld\fR, \fB\-\-library\-deviation\fR INTEGER
.IP
Deviation from the expected library length. Default: autodetected.
In range [1..inf].
.HP
\fB\-i\fR, \fB\-\-indel\-rate\fR INTEGER
.IP
Rescue unaligned ends within this percentual number of indels. In
range [0..50]. Default: 25.
.HP
\fB\-ni\fR, \fB\-\-no\-indels\fR
.IP
Turn off the rescue of unaligned ends containing indels.
.IP
Performance Options:
.HP
\fB\-t\fR, \fB\-\-threads\fR INTEGER
.IP
Specify the number of threads to use. In range [1..2048]. Default:
4.
.PP
VERSION
.IP
Last update:
yara_mapper version: 0.9.9 [tarball]
SeqAn version: 2.3.1