Sort/Index BAM files.

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Can consume


Can provide



This program sorts and indexes your BAM files, essentially converting a raw-bam-file into a bam-file, which are ready to be used in anvi’o.

If you’re unsure what a BAM file is, check out the bam-file page or this file, written by the developers of samtools. For a description of what indexing a BAM file does, check out the page for raw-bam-file.

To run this program, just provide a path to the bam files that you want to index. For example,

anvi-init-bam raw-bam-file

You can also multithread this to shorten runtime with the flag -T followed by the desired number of threads if your system is capable of this.

To see it in action (plus a description on how to run it on an entire folder), check out this page.

Edit this file to update this information.

Additional Resources

Are you aware of resources that may help users better understand the utility of this program? Please feel free to edit this file on GitHub. If you are not sure how to do that, find the __resources__ tag in this file to see an example.