Whole-exome sequencing in children with dyslexia implicates rare variants in CLDN3 and ion channel genes (code)

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.