BamUtil
From Genome Analysis Wiki
Jump to navigationJump to searchThe printable version is no longer supported and may have rendering errors. Please update your browser bookmarks and please use the default browser print function instead.
bam Executable
The bam executable has the following functions.
- Read and Validate a SAM/BAM file
- Read a SAM/BAM file and write as a SAM/BAM file
- Dump a BAM index file into an easy to read text version
- Read an indexed BAM file reference by reference id -1 to 22 and write it out as a SAM/BAM file
Read and Validate a SAM/BAM file
The validate option on the bam executable validates a SAM/BAM file.
The validation checks that the file is sorted as specified in the user options. Default is unsorted, in which case, no order validation is done.
NOTE: Currently the only validation that is done is that the file is sorted as specified in the user specified options.
Usage
./bam validate --in <inputFile> [--so_flag|--so_unsorted|--so_coord|--so_query]
Return Value
- 0: all records are successfully read, are valid, and are properly sorted.
- non-0: at least one record was not successfully read, not valid, or not properly sorted.
Example Output
Read a SAM/BAM file and write as a SAM/BAM file
Usage
./bam <inputFile> <outputFile.sam/bam>
Return Value
Example Output
Dump a BAM index file
Usage
./bam dump_index <bamIndexFile>
Return Value
- -1 if the bam index file could not be opened.
- 0 if the bam index file could be opened.
Example Output
Read & Write indexed BAM file
Usage
./bam read_indexed_bam <inputFilename> <outputFile.sam/bam> <bamIndexFile>
Return Value
- 0
