SAM to sorted BAMv2
SAM to sorted BAMv2
Create a position-sorted BAM file from a SAM alignment file
App Creator
Roger Barthelson
Quick Start
- To use SAM to sorted BAMv2, import your data in SAM format.
- Resources: http://www.htslib.org/
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 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.
Related Tutorials
Discover Variants Using SAM Tools (Workflow Tutorial)