---
name: "samtools-faidx"
section: "1"
platform: "linux"
package: "samtools"
version: "1.21-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/samtools-faidx"
---

# samtools-faidx(1)

indexes or queries regions from a fasta file

## NAME

samtools-faidx - indexes or queries regions from a fasta file

## SYNOPSIS

samtools faidx *ref.fasta* \[*region1* \[...\]\]

## DESCRIPTION

Index reference sequence in the FASTA format or extract subsequence from indexed reference sequence. If no region is specified, **faidx** will index the file and create *\<ref.fasta\>.fai* on the disk. If regions are specified, the subsequences will be retrieved and printed to stdout in the FASTA format.

The input and output can be files compressed in the **BGZF** format. When output is compressed, the default compression level is 4.

The sequences in the input file should all have different names. If they do not, indexing will emit a warning about duplicate sequences and retrieval will only produce subsequences from the first sequence with the duplicated name.

FASTQ files can be read and indexed by this command.  Without using **--fastq** any extracted subsequence will be in FASTA format.

## OPTIONS

- **-o, --output** *FILE*

  Write FASTA to file rather than to stdout. With .gz, .bgz, .bgzf file extensions the output will be **BGZF** compressed.

- **-n, --length** *INT*

  Length for FASTA sequence line wrapping.  If zero, this means do not line wrap.  Defaults to the line length in the input file.

- **-c, --continue**

  Continue working if a non-existent region is requested.

- **-r, --region-file** *FILE*

  Read regions from a file. Format is chr:from-to, one per line.

- **-f, --fastq**

  Read FASTQ files and output extracted sequences in FASTQ format.  Same as using samtools fqidx.

- **-i, --reverse-complement**

  Output the sequence as the reverse complement. When this option is used, “/rc” will be appended to the sequence names. To turn this off or change the string appended, use the **--mark-strand** option.

- **--mark-strand TYPE**

  Append strand indicator to sequence name.  TYPE can be one of:

  - **rc**

    Append '/rc' when writing the reverse complement.  This is the default.

  - **no**

    Do not append anything.

  - **sign**

    Append '(+)' for forward strand or '(-)' for reverse complement.  This matches the output of “bedtools getfasta -s”.

  - **custom,\<pos\>,\<neg\>**

    Append string \<pos\> to names when writing the forward strand and \<neg\> when writing the reverse strand.  Spaces are preserved, so it is possible to move the indicator into the comment part of the description line by including a leading space in the strings \<pos\> and \<neg\>.

- **--fai-idx FILE**

  Read/Write to specified index file.

- **--gzi-idx FILE**

  Read/Write to specified compressed file index (used with .gz files).

- **-h, --help**

  Print help message and exit.

- **--output-fmt-option** *OPT=VAL*

  Set the output format options, level=0..9 for compression level 0 to 9.

- **-@, --threads** *N*

  Set the number of extra threads for operations on compressed files.

## AUTHOR

Written by Heng Li, with modifications by Andrew Whitwham and Robert Davies, all from the Sanger Institute.

## SEE ALSO

[*samtools*(1)](/samtools/1.md), [*samtools-fasta*(1)](/samtools-fasta/1.md), [*samtools-fqidx*(1)](/samtools-fqidx/1.md), [*samtools-fastq*(1)](/samtools-fastq/1.md)

Samtools website: \<http://www.htslib.org/\>