domains / families / science / filtering-best-practices
Filters germline and somatic variant callsets at the site and genotype level with GATK VQSR (VQSLOD, truth-sensitivity tranches), VETS/ScoreVariantAnnotations, NVScoreVariants, hard filters with per-annotation thresholds, and bcftools/cyvcf2 expressions, plus Ti/Tv-based QC. Use when deciding between VQSR, hard filtering, and ML recalibration by cohort size and platform, setting SNP vs indel thresholds, replicating the missing-annotation-passes rule so hom-alt sites survive, applying genotype-level GQ/DP filters, or validating filter impact. Not for VCF normalization (see variant-calling/variant-normalization) or summary statistics (see variant-calling/vcf-statistics).
The two skills cover the same domain but have distinct, non-overlapping material. The first copy (OpenClaw) provides a concise decision tree and a comprehensive reference for GATK hard filter thresholds and bcftools expression syntax. The second copy (GPTomics) provides a deeper methodological framework, including VQSR mechanics, VETS, NVScoreVariants, and specific warnings about version compatibility and the 'missing-annotation-passes' rule. Neither is a simple reproduction of the other; the first is a 'how-to' reference, while the second is a 'why and when' guide with more advanced tooling. Combining them provides a complete skill that covers both the basic execution and the advanced decision-making logic.