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

       Written by Heng Li from the Sanger Institute.

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

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

-r         Remove secondary and unmapped reads.  If one of a pair is removed, the PAIRED flag will not be
                  unset  on  the remaining read.  This is a change from the older behaviour in samtools versions
                  up to 1.20.

       -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.

       -M         Fix any base modification tags (MM, ML and MN).  If we have secondary  alignments  with  hard-
                  clipping  and  the  hard clipped reads do not have an MN tag then we use the base modification
                  tags in the primary alignment to clip the secondary alignment modifications, adding MN tags in
                  the process.

                  This also does other sanity checks on the consistency of these tags.

       -u         Output uncompressed BAM or CRAM.

       -OFORMAT  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.

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

       -zFLAGs,--sanitizeFLAGs
                  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 -zoff to disable this.

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

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

samtools-1.21                                   12 September 2024                            samtools-fixmate(1)

       samtools fixmate [-rpcmu] [-Oformat] in.nameSrt.bamout.bam