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]
       [...]

DESCRIPTION

       Removes the alignment information added by the aligner. CIGAR and reference data are removed.  Flags  are
       updated  as  unmapped  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.  Supplimentary and  secondary
       alignment data are discarded.

       Aux  tags  that will be retained in output is controlled by keep-tag and remove-tag/x. These options take
       tags as comma separated lists.

       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.

       -@,--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

       Written by Vasudeva Sarma of the Wellcome Sanger Institute.

SEE ALSO

       samtools(1), samtools-collate(1)

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

samtools-1.19.2                                  24 January 2024                               samtools-reset(1)