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/>