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Samtools 1.7 SAM to sorted BAM 

Community rating: ????? 

Create a position- sorted BAM file from a SAM alignment file

Samtools 1.7 SAM to sorted

BAMv2Community rating: ?????



Create a position-sorted BAM file from a SAM alignment file

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-SAMtoSortedBAM.

Input File(s)

Use  BowtieOutput.sam from the directory listed above. 

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.

  • Default parameters only, no further configuration needed.

Output File(s)

Expect a BAM file named after the input as output. For the test case, the output file you will find in the example_data directory is named sorted.bam.

Tool Source for App

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