From Genome Analysis Wiki
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10:57, 6 April 2010
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== Read and Validate a SAM/BAM file ==
The <code>validate</code> 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 ===
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