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Samtools 1.7 view - Filter mapped or unmapped reads


Test Data


Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> Samtools_view

Input File(s)

Use FILE NAME HERE sample_1.bam in the directory above as your input file. 


  • Select BAM format from the drop down box.
  • Select 'remove unmapped reads' under the 'options' section

Output File(s)

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.