adrisede / DrukBam

DrukBam

DrukBam is a program for plotting alignment files (.bam) for all comandline aficionados.

DrukBam can be used with or without a reference fasta file and allows fast plotting multiple variants or regions of interest. Please provide feedback like bugs or options you might miss, I wrote this programm because I did not found a convicning tool to provide fast plotting of alignemnts withput using a GUI like in IGV or Tablet.

reference free

including a reference

split reads by strand

bigger span

changing plt style to dark or bmh

highlight soft/hard clipped reads by threshold --> visualize insertion points

Installing

requirements

• pysam
• pandas
• matplotlib
• tqdm

installation

DrukBam is available via pypi:

pip install drukbam==1.1.4

docker image

docker pull stephanholgerdrukewitz/drukbam:1.1.4

docker usage

docker  run -it --rm -v $PWD:/data drukbam:1.1.4 DrukBam region  -s 281367 -e 281468   -c 19 -b /data/test_data/test_small.bam  --outfmt png  -i example_out_small --maxcoverage 60 --outlineoff

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❗ ❗ versions <1.1.4 are deprecated and should not be used anymore ❗ ❗

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Usage

DrukBam vcf

usage: DrukBam vcf [-h] -b BAM -v VCF [-p PADDING] [--highlight]
                   [--threads THREADS] [--maxcoverage MAXCOVERAGE]
                   [--direction] [--schematic] [--style STYLE] [--fasta FASTA]
                   [--outputdir OUTPUTDIR] [-i ID] [--chunksize CHUNKSIZE]
                   [--outfmt OUTFMT] [--outlineoff]

optional arguments:
  -h, --help            show this help message and exit

required arguments:
  -b BAM, --bam BAM     Pos. sorted and indexed bam file
  -v VCF, --vcf VCF     vcf file with variants of interest
  -p PADDING, --padding PADDING
                        number of nt around the variant
  --highlight           highlight the position of interest

optional arguments:
  --threads THREADS     number of cpu's to run in paralell, ROI <1000 will
                        always use 1 core
  --maxcoverage MAXCOVERAGE
                        max cov to plot
  --direction           split reads by forward and reverse
  --schematic           plot no nucleotide, recommended for ROI>1000
  --style STYLE         different style options for the plot, provide .ini
                        file
  --fasta FASTA         fasta file for reference related plotting
  --outputdir OUTPUTDIR
                        directory for output
  -i ID, --id ID        output filename
  --chunksize CHUNKSIZE
                        max size of visualized area, can be increases but will
                        sow down calculation
  --outfmt OUTFMT       format of plot, choose between pdf,svg,png
  --outlineoff          plotting of read outline

DrukBam region

usage: DrukBam region [-h] -b BAM -c CHROMOSOME -s START -e END
                    [--threads THREADS] [--maxcoverage MAXCOVERAGE]
                    [--direction] [--schematic] [--style STYLE]
                    [--fasta FASTA] [--outputdir OUTPUTDIR] [-i ID]
                    [--chunksize CHUNKSIZE] [--outfmt OUTFMT] [--outlineoff]

optional arguments:
-h, --help            show this help message and exit

required arguments:
-b BAM, --bam BAM     Pos. sorted and indexed bam file
-c CHROMOSOME, --chromosome CHROMOSOME
                      name of chromosome/contig
-s START, --start START
                      start of region of interest
-e END, --end END     end of the region of interest

optional arguments:
--threads THREADS     number of cpu's to run in paralell, ROI <1000 will
                      always use 1 core
--maxcoverage MAXCOVERAGE
                      max cov to plot
--direction           split reads by forward and reverse
--schematic           plot no nucleotide, recommended for ROI>1000
--style STYLE         different style options for the plot, provide .ini
                      file
--fasta FASTA         fasta file for reference related plotting
--outputdir OUTPUTDIR
                      directory for output
-i ID, --id ID        output filename
--chunksize CHUNKSIZE
                      max size of visualized area, can be increases but will
                      sow down calculation
--outfmt OUTFMT       format of plot, choose between pdf,svg,png
--outlineoff          plotting of read outline

Usage Examples:

The following command will create an image of that region:

DrukBam region  -s 281367 -e 281468   -c 19 -b test_data/test_small.bam  --outfmt png  -i example_out --maxcoverage 60 --outlineoff --fasta test_data/chr19_first500k.fasta

The arguments used above are:

-s start of ROI

-e end of ROI

-c chromosome of ROI

-b alignment file, sorted and indexed

--outfmt format of plot

-i ID which is used for naming the plot

--maxcoverage yaxis max of plot

--outlineoff dont draw outlines around every read

--fasta location of ref. fasta

The following command will plot all positions in a vcf file:

DrukBam vcf -b test_data/test_small.bam  -v example.vcf --padding 100  -i example_vcf --maxcoverage 60  --fasta test_data/chr19_first500k.fasta --threads 12

The arguments used above are:

-b alignment file, sorted and indexed

-v vcf file

-i ID which is used for naming the plot

--maxcoverage yaxis max of plot

--fasta location of ref. fasta

--threads number of cpu's to use,

Style changes:

• color and style can be changed using the --style option and providing a style.ini file
• official matplotlib colors are allowed color list
• pltstyle can be changed style list

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