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.
- -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].
- -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/>
12 December 2023 | samtools-1.19 |