repair [options] -i <input_file> -o <output_file>
- -i <string>
- Name of input file. BAM format by default.
- -o <string>
- Name of output file. The output file is in BAM format.
- The input file is in SAM format.
- 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.
- Do not add dummy reads for singleton reads.
Do not include sequences and quality scores of reads in the