samtools-fqidx - Indexes or queries regions from a fastq file
samtools fqidx
ref.fastq [
region1 [...]]
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.
-
-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
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.
Written by Heng Li, with modifications by Andrew Whitwham and Robert Davies, all
from the Sanger Institute.
samtools(1),
samtools-faidx(1),
samtools-fasta(1),
samtools-fastq(1)
Samtools website: <
http://www.htslib.org/>