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

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

9       samtools fixmate [-rpcmu] [-O format] in.nameSrt.bam out.bam
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DESCRIPTION

13       Fill  in  mate  coordinates,  ISIZE and mate related flags from a name-
14       sorted or name-collated alignment.
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OPTIONS

18       -r         Remove secondary and unmapped reads.
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20       -p         Disable FR proper pair check.
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22       -c         Add template cigar ct tag.
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24       -m         Add ms (mate score) tags.  These are used by markdup to  se‐
25                  lect the best reads to keep.
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27       -u         Output uncompressed BAM or CRAM.
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29       -O FORMAT  Write the final output as sam, bam, or cram.
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31                  By  default,  samtools tries to select a format based on the
32                  output filename extension; if output is to  standard  output
33                  or no format can be deduced, bam is selected.
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35       --no-PG    Do not add a @PG line to the header of the output file.
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37       -@, --threads INT
38                  Number  of  input/output compression threads to use in addi‐
39                  tion to main thread [0].
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AUTHOR

43       Written by Heng Li from the Sanger Institute.
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SEE ALSO

47       samtools(1), samtools-markdup(1), samtools-sort(1), samtools-collate(1)
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49       Samtools website: <http://www.htslib.org/>
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53samtools-1.13                     7 July 2021              samtools-fixmate(1)