NAME¶
repair - a component of subread suite
USAGE¶
repair [options]
-i <input_file>
-o
<output_file>
Required arguments:
- -i <string>
- Name of input file. BAM format by default.
- -o <string>
- Name of output file. The output file is in BAM format.
Optional arguments:
- -S
- The input file is in SAM format.
- -c
- Compress the output BAM file. This will reduce the size of BAM file, but
will increase the time of retrieving reads from BAM file.
- -T <int>
- Number of CPU threads. 8 by default.
- -d
- Do not add dummy reads for singleton reads.
- -t
- Do not include sequences and quality scores of reads in the output
file.