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samtools-fixmate(1)	     Bioinformatics tools	   samtools-fixmate(1)

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  se-
		  lect 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 addi-
		  tion to main thread [0].

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/>

samtools-1.12			 17 March 2021		   samtools-fixmate(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | AUTHOR | SEE ALSO

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