AI Summaryname: bio-phasing-imputation-haplotype-phasing description: Phase genotypes into haplotypes using Beagle or SHAPEIT. Resolves which alleles are inherited together on each chromosome. Use when preparing VCF files for imputation, HLA typing, or population genetic analyses requiring phased haplotypes.
Install
Copy this and paste it into Claude Code, Cursor, or any AI assistant:
I want to install the "COPYRIGHT NOTICE" skill in my project. Please run this command in my terminal: # Install skill into your project (3 files) mkdir -p .claude/skills/bio-phasing-imputation-haplotype-phasing && curl --retry 3 --retry-delay 2 --retry-all-errors -o .claude/skills/bio-phasing-imputation-haplotype-phasing/SKILL.md "https://raw.githubusercontent.com/FreedomIntelligence/OpenClaw-Medical-Skills/main/skills/bio-phasing-imputation-haplotype-phasing/SKILL.md" && mkdir -p .claude/skills/bio-phasing-imputation-haplotype-phasing/examples && curl --retry 3 --retry-delay 2 --retry-all-errors -o .claude/skills/bio-phasing-imputation-haplotype-phasing/examples/run_shapeit.sh "https://raw.githubusercontent.com/FreedomIntelligence/OpenClaw-Medical-Skills/main/skills/bio-phasing-imputation-haplotype-phasing/examples/run_shapeit.sh" && curl --retry 3 --retry-delay 2 --retry-all-errors -o .claude/skills/bio-phasing-imputation-haplotype-phasing/usage-guide.md "https://raw.githubusercontent.com/FreedomIntelligence/OpenClaw-Medical-Skills/main/skills/bio-phasing-imputation-haplotype-phasing/usage-guide.md" Then restart Claude Code (or reload the window in Cursor) so the skill is picked up.
Description
The largest open-source medical AI skills library for OpenClaw🦞.
Memory Requirements
| Dataset Size | Beagle Memory | SHAPEIT5 Memory | |--------------|--------------|-----------------| | 1,000 samples | 8 GB | 4 GB | | 10,000 samples | 32 GB | 16 GB | | 100,000 samples | 64+ GB | 32 GB |
Provenance: Authenticated by MD BABU MIA
--> --- name: bio-phasing-imputation-haplotype-phasing description: Phase genotypes into haplotypes using Beagle or SHAPEIT. Resolves which alleles are inherited together on each chromosome. Use when preparing VCF files for imputation, HLA typing, or population genetic analyses requiring phased haplotypes. tool_type: cli primary_tool: beagle measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: • read_file • run_shell_command ---
Download Beagle 5.4
wget https://faculty.washington.edu/browning/beagle/beagle.22Jul22.46e.jar
Basic phasing
java -jar beagle.22Jul22.46e.jar \ gt=input.vcf.gz \ out=phased
Discussion
Health Signals
My Fox Den
Community Rating
Sign in to rate this booster