bio-phasing-imputation-haplotype-phasing

bio-phasing-imputation-haplotype-phasing is a Bioinformatics & life sciences skill for AI agents, published by GPTomics in the bioSkills repository on GitHub. Skillspace rates bio-phasing-imputation-haplotype-phasing B (81/100) and it passed the safety scan; the rating is based on static analysis only.

Estimates haplotype phase from population linkage disequilibrium with SHAPEIT5, SHAPEIT4, Eagle2, or Beagle - turning unphased genotypes (0/1) into phased haplotypes (0|1) for imputation input, compound-heterozygote calls, HLA typing, or population genetics. Covers why statistical phase is an INFERENCE (not a measurement) whose error concentrates at rare variants, why a genome-wide switch-error rate hides catastrophic rare-variant error and must be reported MAC-stratified, the SHAPEIT5 common-scaffold-then-rare design (phase_common, ligate, phase_rare, switch), reference-based vs within-cohort phasing, the build-matched genetic map, chrX male-haploid handling, and the switch-vs-flip-vs-Hamming distinction. Use when phasing genotypes before imputation, for compound-het/ASE/HLA, or benchmarking against trios. Read-backed / molecular phasing (long reads, Hi-C) is long-read-sequencing/haplotype-phasing; panel choice is reference-panels; imputation is genotype-imputation.

Grade

B

Quality

81 / 100

Safety

Passed

GitHub stars

1,025

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