NAME

       samtools fixmate - fills in mate coordinates and insert size fields.

SYNOPSIS

       samtools fixmate [-rpcm] [-O format] in.nameSrt.bam out.bam

DESCRIPTION

       Fill in mate coordinates, ISIZE and mate related flags from a name-sorted alignment.

OPTIONS

       -r         Remove secondary and unmapped reads.

       -p         Disable FR proper pair check.

       -c         Add template cigar ct tag.

       -m         Add  ms  (mate score) tags.  These are used by markdup to select the best reads
                  to keep.

       -O FORMAT  Write the final output as sam, bam, or cram.

                  By default, samtools tries to select a format  based  on  the  output  filename
                  extension;  if output is to standard output or no format can be deduced, bam is
                  selected.

       --no-PG    Do not add a @PG line to the header of the output file.

AUTHOR

       Written by Heng Li from the Sanger Institute.

SEE ALSO

       samtools(1), samtools-markdup(1), samtools-sort(1)

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