samtools-fixmate(1)

fills in mate coordinates and insert size fields.

Section 1 samtools bookworm source

Description

samtools-fixmate

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].

AUTHOR

Written by Heng Li from the Sanger Institute.