OTTER 🦦: Oncology Traces TrackER

A Biohack 2023 project - Analysis of multiple time points of cfDNA from plasma of patients with oncological diagnoses

🦦 consits of filtering, clusterization and variant calling.

Installation

git clone git@github.com:AntonCoon/OncoTracker.git
cd OncoTracker && make

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Requirements

• jre;
• python modules:
  • ipython;
  • pandas;
  • scipy;
  • vcfpy;
  • seaborn.

Alternatively, after installation, a pipeline can be executen within a Docker/Podman container:

docker build -t otter:1 .
docker run -it --rm --mount type=bind,src="$(pwd)",target=/pipeline otter:1

# then run from the contaier
python3 main.py --filter-medium example_data/BH_2/

Usage

python main.py --filter-soft|--filter-medium|--filter-hard| <path/to/folder/with/vcf/files>

A folder with results be created in path/to/folder/with/vcf/files.

Available options are:

• --filter-soft leaves all the variants which occur in at least 2 files;
• --filter-medium leaves only variants which are present in both replicas in at least 2 timepoints;
• --filter-hard leaves only variants which are present in all of the subject's files.

Results description

Results consist of

• filtered_LEVEL.vcf - filtered variants;
• corr_cust.vcf - variants filtered and clustered by correlated in variant allele frequency dynamics (here only variants present in all timepoints are considered);
• SnpEff output:
  • {filtered_LEVEL,corr_clust}_snpEff-ann.vcf - annotated variants;
  • {filtered_LEVEL,corr_clust}_snpEff_genes.txt - gene counts summary;
  • {filtered_LEVEL,corr_clust}_snpEff_summary.html - SnpEff output summary;
• *correlation.pdf - a heatmap of pairwise correlation used for clustering;
• *dendrogram.pdf - a dengrogram with variants colored by cluster cluster.