Samtools 1.7 view - Filter mapped or unmapped reads
Samtools 1.7 view - Filter mapped or unmapped reads
Filter a SAM/BAM file for mapped or unmapped reads.
Quick Start
- To use Samtools 1.7 view - Filter mapped or unmapped reads, import your data in BAM or SAM format.
- Resources:https://github.com/samtools/samtools
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 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
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.