Samtools 1.7 view - Filter mapped or unmapped reads
Filter a SAM/BAM file for mapped or unmapped reads.
- To use Samtools 1.7 view - Filter mapped or unmapped reads, import your data in BAM or SAM format.
Use sample_1.bam in the directory above as your input file.
Parameters Used in App
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.