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samtools-faidx(1)	     Bioinformatics tools	     samtools-faidx(1)

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 for-
	       mat.  Same as using samtools fqidx.

       -i, --reverse-complement
	       Output the sequence as the reverse complement.  When  this  op-
	       tion 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 get-
		      fasta -s".

	       custom,<pos>,<neg>
		      Append string <pos> to names when	 writing  the  forward
		      strand  and <neg>	when writing the reverse strand.  Spa-
		      ces are preserved, so it is possible to move the indica-
		      tor into the comment part	of the description line	by in-
		      cluding a	leading	space in the strings <pos> and <neg>.

	       -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/>

samtools-1.10			6 December 2019		     samtools-faidx(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | AUTHOR | SEE ALSO

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