samtools-fixmate - fills in mate coordinates and insert size fields.
samtools fixmate [
-rpcmu] [
-O format]
in.nameSrt.bam
out.bam
Fill in mate coordinates, ISIZE and mate related flags from a name-sorted or
name-collated alignment.
- -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].
Written by Heng Li from the Sanger Institute.
samtools(1),
samtools-markdup(1),
samtools-sort(1),
samtools-collate(1)
Samtools website: <
http://www.htslib.org/>