domains / families / data / vcf-statistics
Compute and interpret VCF quality-control metrics (Ti/Tv, het/hom, novel/known, missingness, HWE, contamination, relatedness) with bcftools stats, vcftools, plot-vcfstats, and identity tools (somalier, peddy, KING). Use when judging whether a callset is trustworthy, diagnosing a low Ti/Tv or outlier het/hom sample, deciding whether an HWE deviation is error or biology, screening a cohort for sample swaps/contamination/wrong-sex before analysis, or comparing call sets before and after filtering. Not for applying filters (see variant-calling/filtering-best-practices) or normalizing representation (see variant-calling/variant-normalization).
The two skills cover the same task (VCF statistics and QC) but with different emphases and non-overlapping material. The OpenClaw copy is a broad command reference (bcftools stats, gtcheck, query, cyvcf2) with specific expected Ti/Tv ranges and plotting steps. The GPTomics copy is a decision-oriented QC guide that adds a governing principle (cohort-relative interpretation, order of operations, identity as a graph problem), a detailed decision table for interpreting deviations, version compatibility notes, and additional tools (vcftools, somalier, peddy, KING). Neither is a strict reproduction of the other; crowning one would hide the other's unique interpretive framework and tooling.