bio-phasing-imputation-reference-panels
Download, prepare, and manage reference panels for phasing and imputation. Covers 1000 Genomes, HRC, and TOPMed panels. Use when setting up imputation infrastructure or selecting appropriate reference panels for target populations.
npx skills add BioTender-max/awesome-bio-agent-skills --skill reference-panels --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: bcftools 1.19+, picard 3.1+ Before using code patterns, verify installed versions match. If versions differ: - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Reference Panels **"Set up reference panels for imputation"** → Download, prepare, and manage reference panels (1000 Genomes, HRC, TOPMed) for genotype phasing and imputation, including population subsetting and format conversion. - CLI: `bcftools view -S panel_samples.txt` for subsetting, `bcftools norm` for normalization ## 1000 Genomes Phase 3 (GRCh38) ```bash # Download from IGSR 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 ``` ## Subset by Population ```bash # Download sample info wget ht
- Version Compatibility
- 1000 Genomes Phase 3 (GRCh38)
- Subset by Population
- Convert to Beagle Format
- Convert to IMPUTE5 Format
- HRC Reference Panel
- TOPMed Reference Panel
- Genetic Maps
- Check Reference Panel
- Lift Over Reference Panel
- Align Study to Reference
- Filter Reference Panel
- Merge Custom Panel with 1000G
- Reference Panel Comparison
Download from IGSR
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
Download sample info
wget http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/1000G_2504_high_coverage.sequence.index
Create population sample lists
grep "EUR" samples.txt | cut -f1 > european_samples.txt
grep "AFR" samples.txt | cut -f1 > african_samples.txtWhat does the bio-phasing-imputation-reference-panels skill do?
Download, prepare, and manage reference panels for phasing and imputation. Covers 1000 Genomes, HRC, and TOPMed panels. Use when setting up imputation infrastructure or selecting appropriate reference panels for target populations.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill reference-panels --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.