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Pipeline for Somatic Variant Calling with WES and WGS data

Please consider using/contributing to https://github.com/nf-core/sarek

Ethnicity Annotation from Whole-Exome and Targeted Sequencing Data

A fork of the project Excavator2 from sourceforge.

This pipeline has moved! Please see:

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

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.

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

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 …

Main Repository for my MASTER'S THESIS PROJECT

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.

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.

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.

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.