Filter a SAM/BAM file for mapped or unmapped reads.
Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> Samtools_view
Use sample_1.bam in the directory above as your 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.
- Select BAM format from the drop down box.
- Select 'remove unmapped reads' under the 'options' section
Expect an output with the name you selected in the app. For the test case, the output file you will get is 'filtered_alignments.bam.