LiteratureScientific Writing & PublishingFreedomIntelligence/OpenClaw-Medical-SkillsLiterature Review

bio-phasing-imputation-reference-panels

Maintainer FreedomIntelligence · Last updated April 1, 2026

Select and prepare reference panels (1KGP, HRC, TOPMed) for imputation.

OpenClawNanoClawDiscoveryReadingbio-phasing-imputation-reference-panels🧠 bioos extended suitebioos extended bioinformatics suiteselect

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-phasing-imputation-reference-panels

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

BASE_URL="http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20201028_3202_phased.
for chr in {1..22}; do wget ${BASE_URL}/CCDG_14151_B01_GRM_WGS_2020-08-05_chr${chr}.filtered.shapeit2-duohmm-phased.vcf.gz wget ${BASE_URL}/CCDG_14151_B01_GRM_WGS_2020-08-05_chr${chr}.filtered.shapeit2-duohmm-phased.vcf.gz.tbi done.
wget http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/1000G_2504_high_coverage.sequence.index.

Source Doc

Excerpt From SKILL.md

Create population sample lists

grep "EUR" samples.txt | cut -f1 > european_samples.txt grep "AFR" samples.txt | cut -f1 > african_samples.txt grep "EAS" samples.txt | cut -f1 > east_asian_samples.txt

Subset reference to specific population

bcftools view -S european_samples.txt
1000GP.chr22.vcf.gz
-Oz -o 1000GP_EUR.chr22.vcf.gz


## Beagle uses VCF directly, but ensure proper format

bcftools view -m2 -M2 -v snps reference.vcf.gz | \
    bcftools annotate --set-id '%CHROM:%POS:%REF:%ALT' | \
    bgzip > reference_beagle.vcf.gz
bcftools index reference_beagle.vcf.gz

Use cases

Use bio-phasing-imputation-reference-panels for manuscript drafting and submission workflows.
Apply bio-phasing-imputation-reference-panels when polishing research communication outputs.