Category
Sam/Bam Manipulation
Usage
samtools fixmate [-rpc] [-O format] in.nameSrt.bam out.bam
Manual
Required arguments
- input.bam file: Input BAM file to fix mate information. The input file must be grouped by read name (e.g. sorted by name). Coordinated sorted input is not accepted.
- output.bam file: Output BAM file with fixed mate information.
Note: As elsewhere in samtools
, use '-' as the filename for stdin/stdout.
Options
- -r: Remove unmapped reads and secondary alignments.
- -p: Disable FR proper pair check
- -c: Add template cigar ct tag
- -m: Add mate score tag
- -u: Uncompressed output
- --no-PG: do not add a PG line
- --input-fmt-option OPT[=VAL]: Specify a single input file format option in the form of OPTION or OPTION=VALUE
- -O, --output-fmt string: Output format ('sam', 'bam', or 'CRAM') for the output file (default: bam).
- --output-fmt-option OPT[=VAL]: Specify a single output file format option in the form of OPTION or OPTION=VALUE
- --reference string: Reference sequence name for header (required if 'input.bam' has no header).
- -@, --threads int: Number of additional threads to use [0]
- --verbosity int: Set level of verbosity
File formats this tool works with
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