cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.18156284
title: HGDP+1KG Phased Reference Panel for Local Ancestry Inference (hg38)

description:  




Phased haplotypes from the joint 1000 Genomes Project (1KG) and Human Genome

 




Diversity Project (HGDP) dataset, processed and QC'd for use as a reference

 




panel in local ancestry inference (LAI) tools including RFMix v2, FLARE,

 




and G-NOMIX.

 




 

 




## Original Data Source

 




 

 




This dataset is derived from the gnomAD v3.1 HGDP+1KG joint callset:

 




- **Source**: gnomAD (Genome Aggregation Database)

 




- **URL**: https://gnomad.broadinstitute.org/downloads#v3-hgdp-1kg

 




- **Google Cloud**: `gs://gcp-public-data--gnomad/resources/hgdp_1kg/phased_haplotypes_v2/`

 




 

 




## Processing Applied

 




 

 




1. Downloaded phased BCF files from gnomAD Google Cloud bucket

 




2. Filtered to biallelic SNPs only

 




3. Applied MAF > 0.5% filter

 




4. Renamed chromosomes to include 'chr' prefix for hg38 compatibility

 




5. Created per-chromosome VCF.gz files with CSI indices

 




 

 




## Samples

 




 

 




- **Total samples**: 4,094 (929 HGDP + 3,165 1KG samples)

 




- **Populations**: 80 populations across 7 continental groups

 




- **Phasing**: SHAPEIT5

 




 

 




## Usage

 




 

 




These files are designed for use with the genotyping_pipeline

 




(https://github.com/chrisrob3312/genotyping_pipeline) Module 7 ancestry

 




estimation, but can be used with any LAI tool that accepts phased VCF input.

 




 

 




## Citation

 




 

 




If you use this dataset, please cite:

 




 

 




1. **gnomAD v3.1**: Karczewski KJ, et al. The mutational constraint spectrum

 




   quantified from variation in 141,456 humans. Nature. 2020;581(7809):434-443.

 




   DOI: 10.1038/s41586-020-2308-7

 




 

 




2. **HGDP**: Bergström A, et al. Insights into human genetic variation and

 




   population history from 929 diverse genomes. Science. 2020;367(6484):eaay5012.

 




   DOI: 10.1126/science.aay5012

 




 

 




3. **1000 Genomes**: 1000 Genomes Project Consortium. A global reference for

 




   human genetic variation. Nature. 2015;526(7571):68-74.

 




   DOI: 10.1038/nature15393

 

4. Joint-called 1KG-HGDP Data Resource**: Koenig Z, Yohannes MT, Nkambule LL, et al. A harmonized public resource of deeply sequenced diverse human genomes. Genome Research. 2024. https://doi.org/10.1101/gr.278378.123

 

 




 




 




 

 




RELATED IDENTIFIERS (add as "References"):

 




- DOI: 10.1038/s41586-020-2308-7 (gnomAD paper)

 




- DOI: 10.1126/science.aay5012 (HGDP paper)

 




- DOI: 10.1038/nature15393 (1000 Genomes paper)

 




- URL: https://github.com/chrisrob3312/genotyping_pipeline (Related software)

 




- URL: https://gnomad.broadinstitute.org/downloads#v3-hgdp-1kg (Source data)
DOI: 10.60712/si-id300332.1
title: StrainInfo SI-ID 300332.1

description: StrainInfo dataset 300332 about a strain of Saccharomyces cerevisiae. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id300333.1
title: StrainInfo SI-ID 300333.1

description: StrainInfo dataset 300333 about a strain of Saccharomyces cerevisiae. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id300378.1
title: StrainInfo SI-ID 300378.1

description: StrainInfo dataset 300378 about a strain of Unidentified. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id300379.1
title: StrainInfo SI-ID 300379.1

description: StrainInfo dataset 300379 about a strain of Unidentified. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id300380.1
title: StrainInfo SI-ID 300380.1

description: StrainInfo dataset 300380 about a strain of Unidentified. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id300381.1
title: StrainInfo SI-ID 300381.1

description: StrainInfo dataset 300381 about a strain of Unidentified. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id300461.1
title: StrainInfo SI-ID 300461.1

description: StrainInfo dataset 300461 about a strain of Fusarium proliferatum. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id300462.1
title: StrainInfo SI-ID 300462.1

description: StrainInfo dataset 300462 about a strain of Fusarium haematococcum. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id300382.1
title: StrainInfo SI-ID 300382.1

description: StrainInfo dataset 300382 about a strain of Unidentified. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id300463.1
title: StrainInfo SI-ID 300463.1

description: StrainInfo dataset 300463 about a strain of Fusarium haematococcum. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id300383.1
title: StrainInfo SI-ID 300383.1

description: StrainInfo dataset 300383 about a strain of Unidentified. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id300384.1
title: StrainInfo SI-ID 300384.1

description: StrainInfo dataset 300384 about a strain of Unidentified. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id300385.1
title: StrainInfo SI-ID 300385.1

description: StrainInfo dataset 300385 about a strain of Unidentified. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id300464.1
title: StrainInfo SI-ID 300464.1

description: StrainInfo dataset 300464 about a strain of Aphanomyces euteiches. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id300465.1
title: StrainInfo SI-ID 300465.1

description: StrainInfo dataset 300465 about a strain of Aphanomyces euteiches. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.15468/dl.qsgwg2
title: Occurrence Download

description: A dataset containing 142903 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Rosa arvensis Huds.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 142903 records from 282 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0346190-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60712/si-id300466.1
title: StrainInfo SI-ID 300466.1

description: StrainInfo dataset 300466 about a strain of Saccharomyces cerevisiae. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id300467.1
title: StrainInfo SI-ID 300467.1

description: StrainInfo dataset 300467 about a strain of Saccharomyces cerevisiae. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id300534.1
title: StrainInfo SI-ID 300534.1

description: StrainInfo dataset 300534 about a strain of Saccharomyces cerevisiae. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.15468/dl.knw6wu
title: Occurrence Download

description: A dataset containing 765310 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "Geometry POLYGON((-94.84772 35.159,-93.4964 35.159,-93.50372 36.69708,-94.89899 36.69708,-94.84772 35.159))",
 "HasCoordinate is true",
 "TaxonKey is Aves",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 765310 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0071673-200221144449610/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60712/si-id300535.1
title: StrainInfo SI-ID 300535.1

description: StrainInfo dataset 300535 about a strain of Saccharomyces cerevisiae. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id300536.1
title: StrainInfo SI-ID 300536.1

description: StrainInfo dataset 300536 about a strain of Saccharomyces cerevisiae. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.15468/dl.ep4z73
title: Occurrence Download

description: A dataset containing 10491 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((4.68086 -37.14318,59.84341 -37.14318,59.84341 -7.49635,4.68086 -7.49635,4.68086 -37.14318))",
 "TaxonKey is Eulophia R.Br."
 ]
}

 The dataset includes 10491 records from 60 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0084729-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60712/si-id300386.1
title: StrainInfo SI-ID 300386.1

description: StrainInfo dataset 300386 about a strain of Unidentified. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.15468/dl.sfnpk6
title: Occurrence Download

description: A dataset containing 126 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Echinops echinatus Roxb.)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 126 records from 16 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0084728-240506114902167/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60712/si-id300387.1
title: StrainInfo SI-ID 300387.1

description: StrainInfo dataset 300387 about a strain of Unidentified. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.15468/dl.3l2lg5
title: Occurrence Download

description: A dataset containing 924 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hylaeus albonitens (Cockerell, 1905)"
 ]
}

 The dataset includes 924 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0023751-190415153152247/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60712/si-id300388.1
title: StrainInfo SI-ID 300388.1

description: StrainInfo dataset 300388 about a strain of Unidentified. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id300389.1
title: StrainInfo SI-ID 300389.1

description: StrainInfo dataset 300389 about a strain of Unidentified. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id300468.1
title: StrainInfo SI-ID 300468.1

description: StrainInfo dataset 300468 about a strain of Saccharomyces cerevisiae. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id300469.1
title: StrainInfo SI-ID 300469.1

description: StrainInfo dataset 300469 about a strain of Saccharomyces cerevisiae. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id300470.1
title: StrainInfo SI-ID 300470.1

description: StrainInfo dataset 300470 about a strain of Saccharomyces cerevisiae. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.15468/dl.t55fst
title: Occurrence Download

description: A dataset containing 40 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Graffenrieda hitchcockii Gleason"
 ]
}

 The dataset includes 40 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0243618-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60712/si-id300471.1
title: StrainInfo SI-ID 300471.1

description: StrainInfo dataset 300471 about a strain of Saccharomyces cerevisiae. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id300537.1
title: StrainInfo SI-ID 300537.1

description: StrainInfo dataset 300537 about a strain of Saccharomyces cerevisiae. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id300538.1
title: StrainInfo SI-ID 300538.1

description: StrainInfo dataset 300538 about a strain of Saccharomyces cerevisiae. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id300539.1
title: StrainInfo SI-ID 300539.1

description: StrainInfo dataset 300539 about a strain of Saccharomyces cerevisiae. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id300540.1
title: StrainInfo SI-ID 300540.1

description: StrainInfo dataset 300540 about a strain of Saccharomyces cerevisiae. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id300390.1
title: StrainInfo SI-ID 300390.1

description: StrainInfo dataset 300390 about a strain of Unidentified. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id300391.1
title: StrainInfo SI-ID 300391.1

description: StrainInfo dataset 300391 about a strain of Unidentified. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id300392.1
title: StrainInfo SI-ID 300392.1

description: StrainInfo dataset 300392 about a strain of Unidentified. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id300393.1
title: StrainInfo SI-ID 300393.1

description: StrainInfo dataset 300393 about a strain of Unidentified. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id300394.1
title: StrainInfo SI-ID 300394.1

description: StrainInfo dataset 300394 about a strain of Unidentified. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.15468/dl.2g8yj6
title: Occurrence Download

description: A dataset containing 337 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Graffenrieda limbata Triana"
 ]
}

 The dataset includes 337 records from 35 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0243625-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60712/si-id300472.1
title: StrainInfo SI-ID 300472.1

description: StrainInfo dataset 300472 about a strain of Saccharomyces cerevisiae. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id300473.1
title: StrainInfo SI-ID 300473.1

description: StrainInfo dataset 300473 about a strain of Saccharomyces cerevisiae. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id300474.1
title: StrainInfo SI-ID 300474.1

description: StrainInfo dataset 300474 about a strain of Saccharomyces cerevisiae. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id300475.1
title: StrainInfo SI-ID 300475.1

description: StrainInfo dataset 300475 about a strain of Saccharomyces cerevisiae. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id300476.1
title: StrainInfo SI-ID 300476.1

description: StrainInfo dataset 300476 about a strain of Saccharomyces cerevisiae. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id300541.1
title: StrainInfo SI-ID 300541.1

description: StrainInfo dataset 300541 about a strain of Saccharomyces cerevisiae. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id300542.1
title: StrainInfo SI-ID 300542.1

description: StrainInfo dataset 300542 about a strain of Komagataella pastoris. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id300543.1
title: StrainInfo SI-ID 300543.1

description: StrainInfo dataset 300543 about a strain of Komagataella pastoris. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id300544.1
title: StrainInfo SI-ID 300544.1

description: StrainInfo dataset 300544 about a strain of Komagataella pastoris. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.60712/si-id300395.1
title: StrainInfo SI-ID 300395.1

description: StrainInfo dataset 300395 about a strain of Unidentified. StrainInfo is a service developed to provide a resolution of microbial strain identifiers by storing culture collection numbers, their relations, and culture-associated data. StrainInfo is part of NFDI4Microbiota consortium.
DOI: 10.15468/dl.pznpjd
title: Occurrence Download

description: A dataset containing 60 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Macrocentrum brevipedicellatum Wurdack"
 ]
}

 The dataset includes 60 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0243653-200613084148143/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.