VCF Variant Filtering
Filters raw genomic VCF files to eliminate sequencing artifacts and generate accurate variant summary statistics.
The VCF Variant Filtering skill provides domain-specific guidance for performing quality control and filtering on raw Variant Call Format (VCF) files produced by tools like GATK, bcftools, and DeepVariant. It guides users through inspecting the FILTER column and QUAL score distributions, applying standard bcftools-based hard filters, interpreting transition-to-transversion (Ts/Tv) benchmarks across WGS and WES assays, and preventing biased metrics caused by sequencing errors and false-positive calls.
Características Principales
01382 GitHub stars
02Detects raw versus pre-filtered VCF files via FILTER column and header inspection
03Applies Phred-scale QUAL and INFO field hard filters using standardized bcftools pipelines
04Evaluates Ts/Tv ratios against whole-genome (WGS) and whole-exome (WES) assay benchmarks
05Tailors filtering decisions based on analysis goals across rare-disease, somatic, or population studies
06Prevents artifact-driven skew in variant counts and allele frequency distributions
Casos de Uso
01Filtering raw germline or somatic call sets before publishing variant summary statistics
02Validating sequencing run quality and caller performance using Ts/Tv ratio benchmarks
03Building reproducible CLI quality control pipelines with bcftools view and bcftools stats