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.

SEE ALSO

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

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