WEP

WEP performs comprehensive Whole Exome Sequencing (WES) analysis of Next Generation Sequencing (NGS) data, producing quality-controlled alignments, SNP and indel calls, and annotated variants for exome-focused studies.

Key Features:

• Complete WES Pipeline: Provides an integrated workflow covering initial quality checks through final variant annotation.
• Input Verification and Quality Control: Implements trimming and filtering processes to ensure integrity and quality of input data.
• Gapped Alignment: Aligns sequencing reads to reference genomes while accommodating gaps in alignments.
• BAM File Handling: Converts, sorts, and indexes BAM files for downstream processing.
• Duplicate Removal: Eliminates redundant reads to improve accuracy of variant calling.
• Indel Optimization and Quality Score Recalibration: Refines alignments around insertion/deletion sites and recalibrates base quality scores.
• SNP and Indel Detection: Identifies single nucleotide polymorphisms (SNPs) and insertion/deletion polymorphisms (indels).
• Variant Annotation: Provides detailed annotations to contextualize genetic variants within biological frameworks.
• Customizable Data Filtering: Applies user-definable thresholds for variant filtering with default values based on recent literature.
• Support for Paired and Single-End Sequencing Data: Processes both paired-end and single-end sequencing reads.
• Cross-Linking and Statistical Analysis via Custom Databases: Stores results in custom databases enabling cross-linking, intersections, and statistical analyses.

Scientific Applications:

• High-penetrance Variant Analysis: Facilitates identification and interpretation of high-penetrance allelic variations and their phenotypic implications.
• Exome-focused Eukaryotic Genomics: Enables extraction of biological insights from exonic regions of eukaryotic genomes.

Methodology:

Computational methods explicitly include trimming and filtering for quality control, gapped alignment to reference genomes, BAM conversion/sorting/indexing, duplicate removal, indel optimization, base quality score recalibration, SNP and indel calling, variant annotation, and storage in custom databases supporting cross-linking and statistical analyses; the tool leverages state-of-the-art algorithms that are regularly updated and tested to maximize variant quality while minimizing artifacts and false positives.