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

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

samtools-1.21                                   12 September 2024                              samtools-faidx(1)