Manual page from samtools-1.19
released on 12 December 2023


samtools faidx – indexes or queries regions from a fasta file


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


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 file can be compressed in the BGZF format.

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.


-o, --output FILE

Write FASTA to file rather than to stdout.

-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:


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


Do not append anything.


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


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.


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


samtools (1), samtools-fasta (1), samtools-fqidx (1), samtools-fastq (1)

Samtools website: <>