NAME

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

SYNOPSIS

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.

-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].

Written by Heng Li from the Sanger Institute.