samtools_Sam_noheader_2Bam
samtools_Sam_noheader_2Bam is a an app for converting sam files that lack the formal headers to the binary bam output.
Quick Start
- To use samtools_Sam_noheader_2Bam, import your Sam file and the index file for the reference sequences used in the alignment that created your Sam file. The index file can be created with samtools_faidx.
- Resources: http://samtools.sourceforge.net/samtools.shtml
Test Data
Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> samtools_Sam_noheader_2Bam.
Input File(s)
Use NC_010473.fa.fai and styec.sam from the directory above as test input.
Parameters Used in App
There are no parameters to set for running this App.
Output File(s)
Expect a output.bam as output. For the test case, the output file you will find in the example_data directory is named Ecoliblat.bam.