NAME

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

SYNOPSIS

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

DESCRIPTION

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

       -u         Output uncompressed BAM or CRAM.

       -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.

       -@, --threads INT
                  Number  of  input/output  compression threads to use in addition to main thread
                  [0].

       -z FLAGs, --sanitize FLAGs
                  Perform basic sanitizing of  records.   FLAGs  is  a  comma-separated  list  of
                  keywords,  defined  in the samtools-view(1) man page.  By default all FLAGs are
                  enabled.  Use -z off to disable this.

AUTHOR

       Written by Heng Li from the Sanger Institute.

SEE ALSO

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

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