Tumor in normal detection

Source code to support the paper: "Extensive mitochondrial population structure and haplotype-specific variation in metabolic phenotypes in the Drosophila Genetic Reference Panel"

Identification of gene-fusions, including EML4-ALK

A framework for generating synthetic genomics data for the evaluation of tumor-only somatic variant calling algorithms.

A framework for generating synthetic genomics data for the evaluation of tumor-only somatic variant calling algorithms.

INDELfindR is an command line tool for detecting complex insertions and deletions (indels) from indexed BAM files.

Obtaining case-associated variants and correspondent genes (from control/case experiments) in BASH/R enviroment

A pipeline to study intratumor heterogeneity (ITH) with Canopy

Pipeline in place at the UGI for DNA level analysis

This repository contains bash shell scripts

Detection of oncogenic and clinically actionable mutations in cancer genomes critically depends on variant calling tools

A streamlined pipeline for germline variant calling on chromosome 11 using GATK. This repository includes workflows for data preprocessing, variant discovery, and annotation, with a focus on understanding genetic variations linked to disease-associated genes.

BSA-QTL Mapping in Drosophila Ananassae

A simple tool for SNP mutation type determination.

NanoSwe: Analysing nanopore (PromethION) data of Swedish genomes

A repository for efficient population genomic analysis using Snakemake workflow.

Management flow using PBS system to analyze sequencing data from Illumina Novaseq6000

interactive variant tables for easy filtering

Pipelines/Wrappers for evaluating the performance of variant callers on tumor/normal RNA-Seq data

This repository contains scripts used to collect and analyze data from whole genome sequences of clinical Streptococcus agalactiae (Group B Strep) isolates for the project described in the following manuscript: Pell, M.E. et al., bioRxiv, 2024-04-01.