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samtools-fqidx(1)	     Bioinformatics tools	     samtools-fqidx(1)

NAME
       samtools	fqidx -	Indexes	or queries regions from	a fastq	file

SYNOPSIS
       samtools	fqidx ref.fastq	[region1 [...]]

DESCRIPTION
       Index  reference	 sequence  in  the FASTQ format	or extract subsequence
       from indexed reference sequence.	If no region is	specified, fqidx  will
       index  the  file	and create _ref.fastq_.fai on the disk.	If regions are
       specified, the subsequences will	be retrieved and printed to stdout  in
       the FASTQ 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.

       samtools	fqidx should only be used on fastq files with a	 small	number
       of  entries.   Trying  to use it	on a file containing millions of short
       sequencing reads	will produce an	index that is almost  as  big  as  the
       original	file, and searches using the index will	be very	slow and use a
       lot of memory.

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

       -n, --length INT
	       Length of FASTQ 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.

       -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>.

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

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

samtools-1.11		       22 September 2020	     samtools-fqidx(1)

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

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