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bamdash

language License: GPL v3 Static Badge DOI PiPy Downloads CONDA CONDA

Overview

BAMdash lets you create interactive coverage plots from your bam file with plotly

  • requires only a .bam, .bai and the reference id to which the reads where mapped
  • create a interactive html for data exploration
  • create a static image (jpg, png, pdf, svg) ready for publication
  • add additional tracks (supported: .vcf, .gb, .bed)
  • annotate tracks with additional information
  • export annoated track data as tabular files (.bed, .vcf) or json (.gb)
  • developed for viral genomics
  • customize all plotting parameters

Feel free to report any bugs or request new features as issues!

Automatic annotation

BAMdash automatically computes serveral statistics:

  • if -bs is > 1 it computes the mean over the bin size in the coverage plot
  • for each track it computes recovery and mean coverage (set -c for the min coverage) for each element in the track
  • if a *.vcf is provided it annotates TRANSITION/TRANSVERSION and type of exchange (SNP, DEL, INS)

If a *.gband *.vcf is provided BAMdash computes if the mutations could have been caused by APOBEC deamination. Moreover, it annotates the aminoacid exchange and the effect in the CDS (inspired by but not as powerful as snpeff). SNP and INDEL vcf annotation supports:

  • START_LOST: INDEL or SNP start at the CDS and result in a start loss
  • STOP_LOST: INDEL or SNP result in the loss of the stop codon
  • STOP_GAINED: INDEL or SNP result in an additional stop codon
  • SYN: SNP does not lead to an amino acid change
  • NON-SYN: SNP leads to an amino acid change
  • AC_INSERTION: INS that does not change already present amino acids
  • AC_CHANGE+AC_INSERTION: INS where the affected codon is also non-syn
  • AC_DELETION: DEL that does not change already present amino acids
  • AC_CHANGE+AC_DELETION: DEL where the affected codon is also non-syn
  • FRAMESHIFT: INDEL that leads to a frameshift

The nomenclature for the aminoacid effect is pretty simplified:

  • A58Y - Exchange at pos 58 from A to Y
  • A58YY- Exchange at pos 58 from A to Y and insertion of an additional Y
  • AF58Y- Exchange at pos 58 from A to Y and deletion of the following F
  • A58fsX - Frameshift at pos 58

Example

example

Installation

via pip (recommened):

pip install bamdash

via conda:

conda install -c bioconda bamdash

from this repo:

git clone https://github.com/jonas-fuchs/BAMdash
cd BAMcov

and then install BAMdash with:

pip install -r requirements.txt

or:

pip install .

That was already it. To check if it worked:

bamdash -v

You should see the current BAMdash version.

Usage

usage: 	

bamdash -b bam_file_path -r reference_id [additional arguments]
full usage:

  -h, --help            show this help message and exit
  -b  , --bam           bam file location
  -r  , --reference     seq reference id
  -q 15, --quality-threshold 15
                        qaulity threshold for reads
  -bs  , --binsize      bins for the coverage plot
  -t [track_1 ...], --tracks [track_1 ...]
                        file location of tracks
  -c 5, --coverage 5    minimum coverage
  --slider, --no-slider
                        show slider (default: False)
  -e None, --export_static None
                        export as png, jpg, pdf, svg
  -d px px, --dimensions px px
                        width and height of the static image in px
  --dump, --no-dump     dump annotated track data (default: False)
  -v, --version         show program's version number and exit

Test bamDASH

bamdash -b HEV.bam -r HEV-pat-1 -t HEV.vcf HEVprim.bed HEVamp.bed HEV.gb

Cutomization

BAMcov plotting settings can be adjusted in in the config.py. Therefore, you have to clone this repo.

Go to the configs location:

cd BAMdash/bamdash/scripts/

And open the config.py with a text editor, e.g.:

gedit config.py

and adjust the settings:

# pdf settings
show_log = True

# overall layout
vcf_track_proportion = 0.3
gb_track_proportion = 0.5
bed_track_proportion = 0.2
plot_spacing = 0.05

# coverage customize
coverage_fill_color = "rgba(255, 212, 135, 0.2)"
coverage_line_color = "rgba(224, 168, 68, 1)"
average_line_color = "grey"
average_line_width = 1

# track customize
track_color_scheme = "agsunset"  # for mutiple annotations tracks (genebank)
track_color_single = "rgb(145, 145, 145)"  # for single tracks (any rgb value, but no named colors)
strand_types = ["triangle-right", "triangle-left", "diamond-wide"]  # +, -, undefined strand
strand_marker_size = 8
strand_marker_line_width = 1
strand_marker_line_color = "rgba(0, 0, 0, 0.2)"
box_bed_alpha = [0.6, 0.6]  # alpha values for boxes (bed)
box_bed_size = [0.4, 0.4]  # size values for boxes (bed)
box_gb_alpha = [0.6, 0.8]  # alpha values for boxes (gb)
box_gb_size = [0.4, 0.3]  # size values for boxes (gb)

# variant customize
variant_marker_size = 13
variant_marker_line_width = 1
variant_line_color = "black"
stem_color = "grey"
stem_width = 1
snp_color = "grey"
ins_color = "blue"
del_color = "red"

To apply these new settings just repeat the installation procedure in the BAMdash dir:

pip install .

Important disclaimer: The code is under the GPLv3 licence. The code is WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.