Samtools 1.7 SAM to BAM format conversion
Samtools 1.7 SAM to BAM format conversion
Create a BAM file from a SAM alignment file
Quick Start
To use SAM to BAM, import your data in SAM format.
Resources: http://www.htslib.org/
Test Data
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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 called output.bam as output. For the test case, the output file you will find in the example_data directory is named output.bam.