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Found 3 Skills
Production-ready VCF processing, variant annotation, mutation analysis, and structural variant (SV/CNV) interpretation for bioinformatics questions. Parses VCF files (streaming, large files), classifies mutation types (missense, nonsense, synonymous, frameshift, splice, intronic, intergenic) and structural variants (deletions, duplications, inversions, translocations), applies VAF/depth/quality/consequence filters, annotates with ClinVar/dbSNP/gnomAD/CADD via ToolUniverse, interprets SV/CNV clinical significance using ClinGen dosage sensitivity scores, computes variant statistics, and generates reports. Solves questions like "What fraction of variants with VAF < 0.3 are missense?", "How many non-reference variants remain after filtering intronic/intergenic?", "What is the pathogenicity of this deletion affecting BRCA1?", or "Which dosage-sensitive genes overlap this CNV?". Use when processing VCF files, annotating variants, filtering by VAF/depth/consequence, classifying mutations, interpreting structural variants, assessing CNV pathogenicity, comparing cohorts, or answering variant analysis questions.
Expert-level biology, biotechnology, genetics, bioinformatics, and computational biology
Identify and prioritize causal variants at GWAS loci using statistical fine-mapping and locus-to-gene predictions. Computes posterior probabilities for causal variants, links variants to genes via L2G predictions, annotates functional consequences, and suggests validation strategies. Use when asked to fine-map GWAS loci, prioritize causal variants, identify credible sets, or link GWAS signals to causal genes.