REPAIR(1) | User Commands | REPAIR(1) |
NAME¶
repair - Find reads that are from the same pair in the input and then place them next to each other in the output. A dummy read is added for each singleton read that does not have a pair. The output file is compatible with featureCounts program
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.
repair Version 2.0.1
- Find reads that are from the same pair in the input and then place them next
to each other in the output. A dummy read is added for each singleton read that does not have a pair. The output file is compatible with featureCounts program.
May 2020 | repair 2.0.1+dfsg |