| | By default, either '/1' or '/2' is added to the end of read names where the corresponding
READ1 or READ2 FLAG bit is set. Using -n causes read names to be left as they are.
|
| | Always add either '/1' or '/2' to the end of read names even when put into different files.
|
| | Use quality values from OQ tags in preference to standard quality string if available.
|
| | write singleton reads to FILE. |
| | Copy RG, BC and QT tags to the FASTQ header line, if they exist.
|
| | Specify a comma-separated list of tags to copy to the FASTQ header line, if they exist.
TAGLIST can be blank or `*` to indicate all tags should be copied to the output. If using `*`,
be careful to quote it to avoid unwanted shell expansion.
|
| | Write reads with the READ1 FLAG set (and READ2 not set) to FILE instead of outputting them.
If the -s option is used, only paired reads will be written to this file.
|
| | Write reads with the READ2 FLAG set (and READ1 not set) to FILE instead of outputting them.
If the -s option is used, only paired reads will be written to this file.
|
| | Write reads with either READ1 FLAG or READ2 flag set to FILE instead of outputting them to stdout.
This is equivalent to -1 FILE -2 FILE.
|
| | Write reads where the READ1 and READ2 FLAG bits set are either both set or both unset to FILE
instead of outputting them.
|
| | Only output alignments with all bits set in INT present in the FLAG field. INT can be specified
in hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/) or in octal by beginning with '0'
(i.e. /^0[0-7]+/). Default: `0`.
|
| | Do not output alignments with any bits set in INT present in the FLAG field. INT can be specified
in hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/) or in octal by beginning with '0'
(i.e. /^0[0-7]+/). This defaults to 0x900 representing filtering of secondary and
supplementary alignments. Default: `0x900`.
|
| | Only output alignments with any bits set in INT present in the FLAG field. INT can be specified
in hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/), in octal by beginning with '0'
(i.e. /^0[0-7]+/), as a decimal number not beginning with '0' or as a comma-separated list of
flag names. Default: `0`.
|
| | Only EXCLUDE reads with all of the bits set in INT present in the FLAG field. INT can be specified
in hex by beginning with '0x' (i.e. /^0x[0-9A-F]+/) or in octal by beginning with '0' (i.e. /^0[0-7]+/).
Default: `0`.
|
| | Only output alignments containing an auxiliary tag matching both TAG and VAL. If VAL is omitted
then any value is accepted. The tag types supported are i, f, Z, A and H. "B" arrays are not
supported. This is comparable to the method used in samtools view --tag. The option may be specified
multiple times and is equivalent to using the --aux_tag_file option.
|
| | Only output alignments containing an auxiliary tag matching TAG and having a value listed in FILE.
The format of the file is one line per value. This is equivalent to specifying --aux_tag multiple times.
|
| | Add Illumina Casava 1.8 format entry to header, for example: `1:N:0:ATCACG`.
|
| | set compression level when writing gz or bgzf fastq files. |
| | write first index reads to FILE. |
| | write second index reads to FILE. |
| | Auxiliary tag to find index reads in. Default: `BC`.
|
| | Auxiliary tag to find index quality in. Default: `QT`.
|
| | string to describe how to parse the barcode and quality tags. For example:
* `i14i8`: the first 14 characters are index 1, the next 8 characters are index 2.
* `n8i14`: ignore the first 8 characters, and use the next 14 characters for index 1.
If the tag contains a separator, then the numeric part can be replaced with '*' to mean
'read until the separator or end of tag', for example: `n*i*`.
|