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Samtools 1.7 Sort Bam file
Samtools 1.7 Sort Bam file
- Roger Barthelson
- amcooksey (Unlicensed)
Owned by Roger Barthelson
Last updated: Apr 17, 2018 by amcooksey (Unlicensed)
Samtools 1.7 Sort Bam file
Sort Bam is a function of samtools. Sort alignments by leftmost coordinates or by read names.
Quick Start
- To use Samtools 1.7 Sort Bam file, import your data in bam 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_sort_BAM.
Input File(s)
Use sample_1.bam from the directory above as test input.
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.
Set the output file name by editing the text "output_prefix" or leave it unedited, for an output file named output_prefix.bam.
Output File(s)
Expect a bam as output. For the test case, the output file you will find in the example_data directory is named output_sorted.bam