AgilePindelFilter

AgilePindelFilter filters and prioritizes insertion–deletion (indel) variants from exome and targeted capture sequencing data for clinical and research interpretation.

Key Features:

• Rapid Variant Filtering: Processes indel variant calls to rapidly narrow candidate deleterious mutations relevant to disease diagnosis or prognosis.
• Interactive Variant Analysis: Performs interactive filtering of variant calls after an initial automatic calling step and supports use within a standard Unix pipeline.
• Integration with AgileExomeFilter: Integrates with AgileExomeFilter as part of a suite for coordinated variant filtering and review.
• Scalability and Flexibility: Allows adjustment of filtering parameters to tailor analyses to specific diagnostic or research requirements.

Scientific Applications:

• Clinical diagnostics — cancer predisposition: Applied to targeted capture data from 36 cancer-predisposing genes in a cohort of 128 patients, achieving complete concordance with previous diagnostic data across 793 variant genotypes.
• Clinical diagnostics — primary ciliary dyskinesia (PCD): Applied to whole-exome sequencing for PCD diagnosis and identified a high yield of relevant variants (42%) in the PCD cohort.
• Diagnostic laboratory testing expansion: Supports expansion of testing portfolios by enabling consistent filtering workflows across exome and targeted capture datasets.

Methodology:

An initial automatic variant calling step is followed by interactive filtering using user-defined parameters on outputs from next-generation sequencing (exome and targeted capture) data.