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 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.

OPTIONS

       -o, --output FILE
               Write FASTA to file rather than to stdout.

       -n, --length INT
               Length of FASTA sequence line.  [60]

       -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.

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/>