BAM2PLOT

Plot your bam files!

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