Index BAM--get stats
(SAMTOOLS-0.1.19) Index BAM--get stats
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Perform an idxstats and flagstat analysis of a BAM file
Quick Start
- To use (SAMTOOLS-0.1.19) index BAM--get stats, import your data in BAM format.
Resources: https://github.com/samtools/samtools
Test Data
Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> Index_BAM
Input File(s)
Use sorted.bam from the directory above as test input.
Parameters Used in App
No parameters to set.
Output File(s)
Expect a bam index file, an idxstat file and a flagstat file as outputs. For the test case, the output files you will find in the example_data directory are sorted.bam.bai, sorted.bam.idxstats, and sorted.bam.flagstat