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Samtools 1.7 Sort Bam file

Sort Bam is a function of samtools. Sort alignments by leftmost coordinates . File <out_prefix>.bam will be created.or by read names. 

Quick Start

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_bamBAM.

Input File(s)

Use Ecoliblatsample_1.bam from  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 Ecoliblatoutput_sorted.bam.

Tool Source for App