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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. If one of a pair is re- moved, the PAIRED flag will not be unset on the remaining read. This is a change from the older behaviour in samtools versions up to 1.20. -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. -M Fix any base modification tags (MM, ML and MN). If we have sec- ondary alignments with hard-clipping and the hard clipped reads do not have an MN tag then we use the base modification tags in the primary alignment to clip the secondary alignment modifica- tions, adding MN tags in the process. This also does other sanity checks on the consistency of these tags. -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 out- put 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]. -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. 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-1.23.1 18 March 2026 samtools-fixmate(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | AUTHOR | SEE ALSO
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