Gabriel Mendes, Msc
LinkedIn Profile|Lattes CV|Orcid Profile
Bioinformatician and Data Scientist with +7 years of experience in Computational Biology.
M.Sc. in Genetics (UFMG). I specialize in Data Architecture for biological systems, leveraging Python, R, SQL, and Bash to build reproducible analysis pipelines.
My work bridges the gap between molecular biology and data science, handling complex datasets such as eDNA metabarcoding and variant calling. I focus on statistical rigor, data visualization, and software development to drive biological discovery in any organism or context.
Somatic Variants Consulting (en-US)
About
This project implements a pipeline developed to address the exercise of group 2 “somatic variants”. The objective is to perform somatic variant filtering and preparation for Cancer Genome Interpreter (CGI) analysis.
The script developed is available at /variantes_somaticas/script_variantes_somaticas.sh.
Main objectives:
-
Filters VCF files to retain only clinically relevant somatic variants
-
Applies filters based on population frequency (MAX_AF ≤ 0.01), impact (excluding LOW), clinical significance (pathogenic, not benign), and gene panel matching
-
Generates TSV files formatted for CGI interpretation
-
Processes multiple samples in batch mode
Key steps:
-
Removes variants without consequence annotations (CSQ)
-
Filters variants using Ensembl VEP criteria
-
Extracts and formats variant data into TSV with specific columns
-
Ensures adequate sequencing depth (DP≥20) and allele frequency (AF≥0.1)
The pipeline prepares somatic variant data from annotated VCFs into analysis-ready formats for cancer genomics interpretation.
Instructions
1. Clone the repository:
git clone https://github.com/gbrl-mendes/variantes_somaticas.git
2. Access the script:
cd variantes_somaticas/ && vi script_variantes_somaticas.sh
3.Edit the information:
# Define main directories
BCFTOOLS_DIR="/home/gabriel/downloads/bcftools-1.21"
FILTER_VEP_DIR="/home/gabriel/downloads/ensembl-vep"
PROJECT_DIR="/home/gabriel/projetos/variantes_somaticas"
INPUT_DIR="/home/gabriel/projetos/variantes_somaticas/liftOver-hg38-MF-annotVep"
GENES_FILE="/home/gabriel/projetos/variantes_somaticas/genes/myelofibrosis.txt"
4. Run the script:
/variantes_somaticas$ ./script_variantes_somaticas.sh
The script executes all the filtering steps of the VCF file and the creation of the TSV files so that the results can be interpreted in the Cancer Genome Interpreter (CGI).
The annotation results are made available in the /variantes_somaticas/output directory.
Contact
For more information, contact me through my e-mail 😊