BAM2PLOT

Plot your bam files!

CITATION

If you use bam2plot, please go here to see how to cite!

UPDATE

bam2plot no longer depends on perbase. Now, bam2plot depends on mosdepth

Subcommands

You must call bam2plot with the following subcommands:
   [1]: 'from_bam'
   [2]: 'from_reads'
   [3]: 'guci'

bam2plot from_bam

usage: bam2plot [-h] -b BAM -o OUTPATH [-w WHITELIST] [-t THRESHOLD] [-r ROLLING_WINDOW]
                [-i | --index | --no-index] [-s | --sort_and_index | --no-sort_and_index]
                [-z ZOOM] [-c | --cum_plot | --no-cum_plot] [-p {png,svg,both}]
                [-n NUMBER_OF_REFS]
                sub_command

Plot your bam files!

positional arguments:
  sub_command

options:
  -h, --help            show this help message and exit
  -b BAM, --bam BAM     bam file
  -o OUTPATH, --outpath OUTPATH
                        Where to save the plots.
  -w WHITELIST, --whitelist WHITELIST
                        Only include these references/chromosomes.
  -t THRESHOLD, --threshold THRESHOLD
                        Threshold of mean coverage depth
  -r ROLLING_WINDOW, --rolling_window ROLLING_WINDOW
                        Rolling window size
  -i, --index, --no-index
                        Index bam file
  -s, --sort_and_index, --no-sort_and_index
                        Index and sort bam file
  -z ZOOM, --zoom ZOOM  Zoom into this region. Example: -z='100 2000'
  -c, --cum_plot, --no-cum_plot
                        Generate cumulative plots of all chromosomes
  -p {png,svg,both}, --plot_type {png,svg,both}
                        How to save the plots
  -n NUMBER_OF_REFS, --number_of_refs NUMBER_OF_REFS
                        How many references (chromosomes) to plot

bam2plot from_bam generates coverage plots:

... and if -c is added, cumulative coverage plots for each reference (e.g. chromosomes) for each sample:

If the flag --highlight is given, the regions with a coverage below the --treshold are highlighted:

Below is an example of how bam2plot looks when runned in the terminal:

Examples

Here's an example of how to use the bam2plot from_bam:

bam2plot from_bam --bam input.bam --outpath output_folder --rolling_window 50 --threshold 5 -s -c

bam2plot from_reads

usage: bam2plot [-h] -r1 READ_1 [-r2 READ_2] -ref REFERENCE [-gc | --guci | --no-guci] -o OUT_FOLDER
                [-r ROLLING_WINDOW] [-p {png,svg,both}]
                sub_command

Align your reads and plot the coverage!

positional arguments:
  sub_command

options:
  -h, --help            show this help message and exit
  -r1 READ_1, --read_1 READ_1
                        Fastq file 1
  -r2 READ_2, --read_2 READ_2
                        Fastq file 2
  -ref REFERENCE, --reference REFERENCE
                        Reference fasta
  -gc, --guci, --no-guci
                        Plot GC content? (default: False)
  -o OUT_FOLDER, --out_folder OUT_FOLDER
                        Where to save the plots.
  -r ROLLING_WINDOW, --rolling_window ROLLING_WINDOW
                        Rolling window size
  -p {png,svg,both}, --plot_type {png,svg,both}
                        How to save the plots

bam2plot guci

usage: bam2plot [-h] -ref REFERENCE -w WINDOW -o OUT_FOLDER [-p {png,svg,both}] sub_command

Plot GC content of your reference fasta!

positional arguments:
  sub_command

options:
  -h, --help            show this help message and exit
  -ref REFERENCE, --reference REFERENCE
                        Reference fasta
  -w WINDOW, --window WINDOW
                        Rolling window size
  -o OUT_FOLDER, --out_folder OUT_FOLDER
                        Where to save the plots.
  -p {png,svg,both}, --plot_type {png,svg,both}
                        How to save the plots

Dependencies

bam2plot depends on mosdepth, which you can install via:

conda install -c bioconda mosdepth

Installation

You can install bam2plot using the following pip command:

pip install bam2plot