Variant Filtering

Variant filtering is used to remove low-confidence variants from a VCF file. Working with a filtered dataset increases the reliability and robustness of downstream analyses. In addition, a smaller, high-quality variant set reduces computational time and improves overall performance.

OmicsBox provides two approaches for variant filtering:

• General Variant Filtering: This option allows you to apply customizable thresholds to key variant quality metrics, such as read depth, variant quality score, missing data, allele frequency, and other common filtering criteria. It is suitable for general-purpose filtering of VCF files from a wide range of sequencing experiments.
• dDocent Variant Filtering Pipeline: This option implements the dDocent filtering pipeline, which is specifically designed for VCF files generated from RAD-Seq or GBS-like protocols. It applies a series of recommended filtering steps tailored to reduced-representation sequencing data, helping to retain high-quality variants while accounting for the specific characteristics of these datasets.