Get statistics about a BAM, SAM or CRAM file.
Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> Samtools_mapping_stats.
Use sample_1.bam in the directory above as you input file.
When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.
- Enter 'alignment_stats.txt' in the 'output file name' field.
Expect an output with the name you selected in the app. For the test case, the output file you will get is alignment_stats.txt.