---
name: "yara_mapper"
section: "1"
platform: "linux"
package: "seqan-apps"
version: "2.4.0+dfsg-16"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/yara_mapper"
---

# yara\_mapper(1)

Yara Mapper

## NAME

yara\_mapper - Yara Mapper

## SYNOPSIS

**yara\_mapper** \[*OPTIONS*\] \<*REFERENCE INDEX PREFIX*\> \<*SE-READS FILE*\>\
 **yara\_mapper** \[*OPTIONS*\] \<*REFERENCE INDEX PREFIX*\> \<*PE-READS FILE 1*\> \<*PE-READS FILE 2*\>

## DESCRIPTION

Yara - Yet Another Read Aligner.

See *http://www.seqan.de/projects/yara* for more information.

(c) Copyright 2011-2014 by Enrico Siragusa.

(c) Copyright 2013 by NVIDIA Corporation.

## REQUIRED ARGUMENTS

- **REFERENCE\_INDEX\_PREFIX** *INPUT\_PREFIX*

  An indexed reference genome.

- **READS\_FILE** List of *INPUT\_FILE*'s

  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.

## OPTIONS

- **-h**, **--help**

  Display the help message.

- **--version**

  Display version information.

- **-v**, **--verbose**

  Displays global statistics.

- **-vv**, **--very-verbose**

  Displays extensive statistics for each batch of reads.

### Output Options:

- **-o**, **--output-file** *OUTPUT\_FILE*

  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.

- **-f**, **--output-format** *STRING*

  Specify an output format. Note: when specifying the option                                                             --output-file, the output format is taken from the filename                                                             extension. One of *bam*, *sam*, *sam.bgzf*, *sam.gz*, and *sam.bz2*. Default: *sam*.

- **-rg**, **--read-group** *STRING*

  Specify a read group for all records in the SAM/BAM file. Default: *none*.

- **-sa**, **--secondary-alignments** *STRING*

  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*.

- **-ra**, **--rabema-alignments**

  Output alignments compatible with the                                                                  Read Alignment BEnchMArk (RABEMA).

### Mapping Options:

- **-e**, **--error-rate** *INTEGER*

  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*.

- **-s**, **--strata-rate** *INTEGER*

  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*.

- **-y**, **--sensitivity** *STRING*

  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*.

### Paired-End Mapping Options:

- **-ll**, **--library-length** *INTEGER*

  Expected library length. Default: autodetected. In range \[1..inf\].

- **-ld**, **--library-deviation** *INTEGER*

  Deviation from the expected library length.                                             Default: autodetected. In range \[1..inf\].

- **-i**, **--indel-rate** *INTEGER*

  Rescue unaligned ends within this percentual number of indels. In range \[0..50\]. Default: *25*.

- **-ni**, **--no-indels**

  Turn off the rescue of unaligned ends containing indels.

### Performance Options:

- **-t**, **--threads** *INTEGER*

  Specify the number of threads to use. In range \[1..2048\]. Default: *6*.