CoVarPlot - Covarage Variant Plots for viral whole genome sequencing
This script was created as part of the interARTIC project, and is the code that generates the output plots.
Please cite InterARTIC if you use this. https://github.com/Psy-Fer/interARTIC
Input currently only supports that generated by the artic pipelines, but should work for any virus, or primer scheme you have used.
To generate depth plots from bam files and primer scheme, follow these commands using scripts from the artic pipeline. NB: Copies are in the scripts folder, however these are not mine, and all credit should go to the authors at https://github.com/artic-network/fieldbioinformatics. Seriously, they have done an amazing job.
These are normally run in the regular artic pipeline
# install requirements with python3.6 (not sure if other versions will work, but probably)
python3.6 -m pip install pysam pandas Bio
minimap2 -a -x map-ont -t 4 ~/interartic_bin/primer-schemes/eden/nCoV-2019/V1/nCoV-2019.reference.fasta ../plot_thickens_fastq_pass-NB12.fastq | samtools view -bS -F 4 - | samtools sort -o plot_thickens_sample7_NB12.sorted.bam
python3.6 align_trim.py --normalise 200 ~/interartic_bin/primer-schemes/eden/nCoV-2019/V1/nCoV-2019.scheme.bed --start --remove-incorrect-pairs < plot_thickens_sample7_NB12.sorted.bam | samtools sort -T plot_thickens_sample7_NB12 - -o plot_thickens_sample7_NB12.trimmed.rg.sorted.bam
python3.6 align_trim.py --normalise 200 ~/interartic_bin/primer-schemes/eden/nCoV-2019/V1/nCoV-2019.scheme.bed --remove-incorrect-pairs < plot_thickens_sample7_NB12.sorted.bam | samtools sort -T plot_thickens_sample7_NB12 - -o plot_thickens_sample7_NB12.primertrimmed.rg.sorted.bam
samtools index plot_thickens_sample7_NB12.primertrimmed.rg.sorted.bam
python3.6 make_depth_mask.py --store-rg-depths ~/interartic_bin/primer-schemes/eden/nCoV-2019/V1/nCoV-2019.reference.fasta plot_thickens_sample7_NB12.primertrimmed.rg.sorted.bam plot_thickens_sample7_NB12.coverage_mask.txt
Feedback is welcome.
Use python3, and install the libs needed.
python3 -m pip install matplotlib numpy
You might need tk or somthing like it for the --show option if you don't already have it installed.
usage: covarplot.py [-h] [--version] [-v VCF_FILE] [-d1 DEPTH_FILE_1]
[-d2 DEPTH_FILE_2] [-b BED] [--show] [-s SAVE] [-l]
Plots for interArtic
optional arguments:
-h, --help show this help message and exit
--version Prints version
-v VCF_FILE, --vcf_file VCF_FILE
full path to vcf file (default: None)
-d1 DEPTH_FILE_1, --depth_file_1 DEPTH_FILE_1
full path to depth file 1 (default: None)
-d2 DEPTH_FILE_2, --depth_file_2 DEPTH_FILE_2
full path to depth file 2 (default: None)
-b BED, --bed BED full path to scheme bed file (default: None)
--show Show plot rather than saving it (default: False)
-s SAVE, --save SAVE Save path (default: None)
-l, --log y-axis log scale (default: False)
Example command:
python3 covarplot.py -v example/plot_thickens_sample12_NB12.pass.vcf.gz -d1 example/plot_thickens_sample12_NB12.coverage_mask.txt.nCoV-2019_1.depths -d2 example/plot_thickens_sample12_NB12.coverage_mask.txt.nCoV-2019_2.depths -b example/nCoV-2019.scheme.bed --show -l
You can also run this plot with JUST the -d1 and -d2 flags, or just the -v flag, and get either a coverage or variant plot respectively. Include the -b flag in each though. (I'll make this option too soon)
