samtools-fixmate - Man Page
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/>
Referenced By
samtools(1), samtools-ampliconclip(1), samtools-markdup(1).