HemoMIPs

HemoMIPs analyzes multiplexed Molecular Inversion Probe (MIP) targeted next-generation sequencing (NGS) data to detect genetic variants, assess coverage, and support cohort-level screening such as hemophilia A and B studies.

Key Features:

• Workflow orchestration: Uses Snakemake to run sample demultiplexing, overlap paired-end merging, alignment, MIP-arm trimming, variant calling, coverage analysis, and report generation.
• Variant calling flexibility: Supports GATK v4 and GATK v3 for variant discovery.
• Reporting: Produces an HTML report summarizing covered regions, incomplete or missing areas, called variants, predicted effects, and performance statistics.
• Structural variant probe analysis: Supports analysis of probes designed to capture specific structural variants.
• Sex assignment: Assigns sex using Y-chromosome-unique probes for sample interpretation.
• Imbalanced NGS handling: Processes highly imbalanced targeted NGS datasets typical of MIP experiments.

Scientific Applications:

• Targeted sequencing analysis: Variant detection and coverage assessment in MIP-based targeted NGS panels.
• Cohort screening for hemophilia: Screening patient cohorts for hemophilia A and B to identify benign and likely pathogenic variants.
• Structural variant detection: Detection and interpretation of targeted structural variants captured by specialized probes.
• Sex assignment in genetic studies: Inferring sample sex using Y-chromosome-unique probes for quality control and interpretation.

Methodology:

Snakemake workflow executing sample demultiplexing, overlap paired-end merging, alignment, MIP-arm trimming, variant calling, coverage analysis, and HTML report generation.