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  for FASTQ 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.

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

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

samtools-1.20                                     15 April 2024                                samtools-fqidx(1)