anvi-get-tlen-dist-from-bam

Authors
Requires
Provides
Usage
Example run
Output file
Histogram
Command line interface

Command line usage
Parameters and their descriptions

Additional Resources

Report the distribution of template lengths from a BAM file. The purpose of this is to get an idea about the insert size distribution in a BAM file rapidly by summarizing distances between each paired-end read in a given read recruitment experiment..

🔙 To the main page of anvi’o programs and artifacts.

Authors

A. Murat Eren (Meren)

Requires

bam-file

Provides

This program does not seem to provide any artifacts. Such programs usually print out some information for you to see or alter some anvi’o artifacts without producing any immediate outputs.

Usage

This program may be useful if you are interested in learning the insert size distribution in a given bam-file.

Example run

The most straightforward way to run the program is the following:

anvi-get-tlen-dist-from-bam bam-file

Here is an example output in the terminal:

BAM file .....................................: ./INVERSION-TEST/CP_R03_CDI_C_07_POST.bam
Number of contigs ............................: 8
Number of reads ..............................: 2,331,062
Minimum template length frequency ............: 10
Maximum template length to consider ..........: 500,000


WARNING
===============================================
Some of your contigs, 2 of 8 to be precise, did not seem to have any template
lenght data. There are many reasons this could happen, including a very high
`--min-tlen-frequency` parameter for BAM files with small number of reads. But
since there are some contigs that seem to have proper paired-end reads with
template lengths, anvi'o will continue reporting and put zeros for contigs that
have no data in output files.

Output file ..................................: TEMPLATE-LENGTH-STATS.txt


✓ anvi-get-tlen-dist-from-bam took 0:00:05.483682

Output file

The program will report a TAB-delimited output file with the following format:

contig	length	num_reads_considered	mean	mean_Q2Q3	median	min	max	std
B_fragilis_ARW016_000000000001	5526948	2213634	367.6	392.5	393.0	32	71613	663.1
B_fragilis_ARW016_000000000002	3905	634	398.6	398.7	399.0	382	415	7.926
B_fragilis_ARW016_000000000003	4039	588	397.5	397.8	398.0	380	411	7.206
B_fragilis_ARW016_000000000004	3950	524	397.4	397.2	397.0	382	414	7.492
B_fragilis_ARW016_000000000005	911	0
B_fragilis_ARW016_000000000006	647	0
B_fragilis_ARW016_000000000007	12247	1860	394.9	396.7	397.0	99	419	23.61
B_fragilis_ARW016_000000000008	4861	528	396.7	396.7	397.0	384	410	6.746

Histogram

If you run the program with the flag --plot-data, it will attempt to plot a histogram for all contigs in the BAM file.

The plotting function requires an additional Python library, plotext, to be installed. While it is not a part of the default anvi’o distirbution, you can install it in your environment by running pip install plotext.

Here is an example run:

anvi-get-tlen-dist-from-bam C09F039427B4.bam \
                            --plot-data

And the result in the terminal:

The histogram may require additional filters to avoid skewed displays due to outliers. The parameters --max-template-length-to-consider and/or --min-template-length-frequency may be useful for such adjustments. Please see the help menu for their details.

Edit this file to update this information.

Command line interface

The following is the list of parameters and their descriptions in the latest version of anvi-get-tlen-dist-from-bam.

The code that generates this web page ensures that this information is the latest available in 9-dev (eunice). Which means, in some cases the information in this section (generated automatically) might be more comprehensive or up-to-date compared to the descriptions above (written by humans).

Command line usage

anvi-get-tlen-dist-from-bam [-h] [--min-template-length-frequency MIN_TEMPLATE_LENGTH_FREQUENCY] [--max-template-length-to-consider MAX_TEMPLATE_LENGTH_TO_CONSIDER] [-o FILE_PATH] [--plot-data] BAM_FILE

Parameters and their descriptions

positional arguments

BAM_FILE required: An indexed BAM file

INPUT OPTIONS Things you don't care but should.

--min-template-length-frequency MIN_TEMPLATE_LENGTH_FREQUENCY: How many times a template lenght should be observed to be considered as a viable template lenght? If this number is zero, you will have an extremely large number template lengths that will likely be due to noise. This number can be best set as a function of the total number of mapped reads in a bam file. The default value is set with the assumption that you have millions of reads in the BAM file. Default: 10
--max-template-length-to-consider MAX_TEMPLATE_LENGTH_TO_CONSIDER: Some paired end reads will map incredibly distant locations given the linear sequences you have used for read recruitment if the DNA templates were circular in the sample used for sequencing. Which is a beautiful thing, but can ruin your histogram. Using this parameter, you can discard paired end reads that are extremely distant from one another. Default: 500000

OUTPUT OPTIONS Output options.

-o, --output-file FILE_PATH: File path to store results.
--plot-data: In addition to providing you with a TAB-delimited output file, anvi'o can also try to plot a summary histogram for the template length distribution across ALL contigs in a given BAM file

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.