Frames the phasing/imputation pipeline before any tool runs: phasing and imputation are one Li-Stephens copying HMM (recombination is the transition, mutation the emission, the genetic map and Ne set the rates), imputation's honest output is a dosage with a self-estimated quality (INFO/R2/DR2) not a hard genotype, and the stages are ordered and each fails silently (QC, align build and strand to the panel, phase, impute per chromosome, filter by INFO/R2 plus a MAF floor, carry dosages to GWAS). Covers the strategy fork (array vs low-coverage WGS plus genotype-likelihood imputation), why the panel ancestry is the prior, and why a flipped strand or build mismatch destroys accuracy without an error. Use when deciding a genotyping strategy, sequencing the pipeline, choosing array vs low-coverage WGS, or diagnosing silently-wrong imputation. Mechanics route to reference-panels, haplotype-phasing, genotype-imputation, imputation-qc; read-backed phasing is long-read-sequencing/haplotype-phasing.
Install with
Claude CodeCodexCursorGitHub CopilotGemini CLI
Supported by the Atlas install prompt. Skill-specific requirements vary.
Skill stats
Skills1CategoryGeneralStars0
About this skill
Frames the phasing/imputation pipeline before any tool runs: phasing and imputation are one Li-Stephens copying HMM (recombination is the transition, mutation the emission, the genetic map and Ne set the rates), imputation's honest output is a dosage with a self-estimated quality (INFO/R2/DR2) not a hard genotype, and the stages are ordered and each fails silently (QC, align build and strand to the panel, phase, impute per chromosome, filter by INFO/R2 plus a MAF floor, carry dosages to GWAS). Covers the strategy fork (array vs low-coverage WGS plus genotype-likelihood imputation), why the panel ancestry is the prior, and why a flipped strand or build mismatch destroys accuracy without an error. Use when deciding a genotyping strategy, sequencing the pipeline, choosing array vs low-coverage WGS, or diagnosing silently-wrong imputation. Mechanics route to reference-panels, haplotype-phasing, genotype-imputation, imputation-qc; read-backed phasing is long-read-sequencing/haplotype-phasing.
Quick start
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Frames the phasing/imputation pipeline before any tool runs: phasing and imputation are one Li-Stephens copying HMM (recombination is the transition, mutation the emission, the genetic map and Ne set the rates), imputation's honest output is a dosage with a self-estimated quality (INFO/R2/DR2) not a hard genotype, and the stages are ordered and each fails silently (QC, align build and strand to the panel, phase, impute per chromosome, filter by INFO/R2 plus a MAF floor, carry dosages to GWAS). Covers the strategy fork (array vs low-coverage WGS plus genotype-likelihood imputation), why the panel ancestry is the prior, and why a flipped strand or build mismatch destroys accuracy without an error. Use when deciding a genotyping strategy, sequencing the pipeline, choosing array vs low-coverage WGS, or diagnosing silently-wrong imputation. Mechanics route to reference-panels, haplotype-phasing, genotype-imputation, imputation-qc; read-backed phasing is long-read-sequencing/haplotype-phasing.
About this listing
Category
General
Reported license
Not specified
Listing language (estimated)
English
Review status
Not individually reviewed
Agent compatibility
Atlas installation supports Claude Code, Codex, and Cursor. Skill-specific dependencies and features are checked during setup.
Claude Code
Codex
Cursor
GitHub Copilot
Gemini CLI