Ubuntu Manpage: samtools-reset - removes the alignment information added by aligners and updates flags accordingly

NAME

       samtools-reset - removes the alignment information added by aligners and updates flags accordingly

SYNOPSIS

       samtools  reset  [-o  FILE] [-x,--remove-tag STR] [--keep-tag STR] [--reject-PG pgid] [--no-RG] [--no-PG]
       [--dupflag] [...]

DESCRIPTION

       Removes the alignment information added by the aligner. CIGAR and reference data are removed.  Flags  are
       updated  as unmapped, non-duplicate and as not a proper pair.  If the alignment was in reverse direction,
       data and its quality values are reversed and complemented and the reverse flag is  reset.   Supplementary
       and secondary alignment data are discarded.

       Aux  tags  that  will be retained in output can be controlled by keep-tag and remove-tag/x. These options
       take tags as comma separated lists.  Aux tags AS, CC, CG, CP, H1, H2, HI, H0, IH, MC, MD, MQ, NM, SA  and
       TS are removed by default, this can be overridden using keep-tag.

       PG  and  RG  tags  from input are written on the output by default.  CO lines are not retained after this
       operation.

       The sort order is unchanged, so users may consider combining this with samtools collate or sort -n if  it
       is a requirement to group pairs of sequences together.

OPTIONS

-o FILE Output file to which reset data is to be written. If not given, standard output will be used.

-x STR, --remove-tag STR
Read tag(s) to exclude from output (repeatable) [null]. This can be a single tag or a comma
separated list. Alternatively the option itself can be repeated multiple times.

If the list starts with a `^' then it is negated and treated as a request to remove all tags
except those in STR. The list may be empty, so -x ^ will remove all tags.

--keep-tag STR
This keeps only tags listed in STR and is directly equivalent to --remove-tag ^STR. Specifying
an empty list will remove all tags. If both --keep-tag and --remove-tag are specified then
--keep-tag has precedence.

--reject-PG pgid
The PG line which has the ID matching pgid and all subsequent PG lines will be removed. If the
option itself is absent, the default, all PG entries will be in output.

--no-RG RG lines in input will be discarded with this option. By default, RG lines will be present in
output.

With this option, RG aux tags will also be discarded.

--no-PG Do not add a @PG line to the header of the output file listing the reset command. By default the
PG entry for reset will be present in the output.

--dupflag
Keep the duplicate flag as it is. This option is absent by default and alignments are marked non-
duplicates.

-@,--thread N
This gives the number of worker threads to be used.

-O,--output-fmt FMT[,options]
Sets the format of the output file and any associated format-specific options. If this option is
not present, the format is identified from the output file name extension.

EXAMPLES

       Basic usage, to reset the data:

         samtools reset -o out.bam in.bam

       To keep aux tags RG and BC in the output:

         samtools reset -o out.sam --keep-tag RG,BC in.bam

       To discard PG entries from 'bwa_index' onwards,

         samtools reset -o out.sam --reject-PG=bwa_index

       To set output format for use within a pipeline:

         samtools collate -O -u input.cram | \
           samtools reset --output-fmt BAM,level=0 | \
           myaligner -I bam -o out.bam

AUTHOR