Manual page from samtools-1.19
released on 12 December 2023


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


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


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



Remove secondary and unmapped reads.


Disable FR proper pair check.


Add template cigar ct tag.


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


Output uncompressed BAM or CRAM.


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.


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.


Written by Heng Li from the Sanger Institute.


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

Samtools website: <>