Research output per year
Research output per year
Description
Whole-Exome Sequencing (WES) Pipeline
This repository contains a modular and reproducible pipeline for Whole-Exome Sequencing (WES) analysis built using Snakemake.
Overview
The pipeline includes the following steps:
Quality Control: Using Trimmomatic to trim raw sequencing reads.
Alignment: Mapping reads to a reference genome using BWA.
Post-alignment Processing:
Merging BAM files with Samtools.
Replacing read groups using Picard.
Marking duplicates.
Base recalibration with GATK.
BAM indexing.
Variant Calling: Using DeepVariant.
Annotation: Annotating variants with Annovar.
Post-processing ANNOVAR Outputs: Parsing, filtering, and merging per-sample ANNOVAR outputs.
This repository contains a modular and reproducible pipeline for Whole-Exome Sequencing (WES) analysis built using Snakemake.
Overview
The pipeline includes the following steps:
Quality Control: Using Trimmomatic to trim raw sequencing reads.
Alignment: Mapping reads to a reference genome using BWA.
Post-alignment Processing:
Merging BAM files with Samtools.
Replacing read groups using Picard.
Marking duplicates.
Base recalibration with GATK.
BAM indexing.
Variant Calling: Using DeepVariant.
Annotation: Annotating variants with Annovar.
Post-processing ANNOVAR Outputs: Parsing, filtering, and merging per-sample ANNOVAR outputs.
| Date made available | 2025 |
|---|---|
| Publisher | GitHub |
Software
- Software
Research output
- 1 Article
-
Whole-exome sequencing in children with dyslexia implicates rare variants in CLDN3 and ion channel genes
Marianski, K., Talcott, J. B., Stein, J., Monaco, A. P., Fisher, S. E., Bishop, D. V. M., Newbury, D. F. & Paracchini, S., 2025, In: Human Genetics.Research output: Contribution to journal › Article › peer-review