anvi-script-get-coverage-from-bam [program]

Get nucleotide-level, contig-level, or bin-level coverage values from a BAM file very rapidly. For other anvi'o programs that are designed to profile BAM files, see anvi-profile and anvi-profile-blitz.

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Authors

Can consume

bam-file collection-txt

Can provide

coverages-txt

Usage

This program gets the coverage values from a bam-file, and puts them into a coverages-txt.

You must provide a BAM file, but there are three ways you can choose contigs to analyze within that file:

1. Give a contig name. Here, you can only report coverage per nucleotide position (In this example, the user is specifically asking for this anyway with the -m flag)

   anvi-script-get-coverage-from-bam -b bam-file \ -c NAME_OF_CONTIG \ -m pos

2. Give a file that contains a list of contigs (one per line; same format as the --contigs-of-interest tag for anvi-profile). Here, you can ask for the contig averages (as in this example) or nucleotide position coverage.

   anvi-script-get-coverage-from-bam -b bam-file \ -l NAME_OF_FILE \ -m contig

3. Give a collection-txt file for the program to determine the coverage for all contigs in those bins. Here, you can ask for the contig averages, nucleotide position coverage or coverage per bin (as in this example).

   anvi-script-get-coverage-from-bam -b bam-file \ -C collection-txt \ -m bin

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.

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