Note: This is a detailed Intro to this project. A brief users guide can be found at users_guide.md

Leveraging WES short reads for PAN-EXOME creation and analysis.

Analysis documentation for research into the variants associated with hyperparathyroidism. Illumina, germline, human, whole exome sequence (WES) data from the CCDHB.

COverage Analysis Tool have been developed in 2016. It aims to automatically find bad quality regions of coding sequences in a set of sequencing data. It includes a graphical interface.

Example workflow to generate a trio VCF from parental data

All QC, annotation, and analyses for IBD exomes

Reference Genome based Exon Phylogeny Pipeline

colorectal cancer

Selects possible pathogenic variants from an Alamut output

Scripts and data processing notes for Russian exome sequencing AF paper

Miscellaneous pipelines for genomics computation analysis in a SGE HPC platform.

Main Repository for my MASTER'S THESIS PROJECT

The transplot package can be used to make multi-track plots of Next Generation Sequencing (NGS) data for gene transcripts, namely for depth of coverage and for the distribution of variants and protein domains.

As part of an overall strategy for improving therapies for childhood cancers, the PPTC seeks to develop models for the types of tumors that will be encountered in early phase clinical testing by establishing patient derived xenografts (PDXs) from high-risk childhood cancers refractory to current standard of care treatments. Genomic profiling of …

Scripts used on a cluster that demonstrate vcf file manipulation and preparation.

Accurate and robust inference of genetic ancestry from cancer-derived molecular data across genomic platforms

This pipeline has moved! Please see:

A fork of the project Excavator2 from sourceforge.

Ethnicity Annotation from Whole-Exome and Targeted Sequencing Data