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Clarify 1KGP dataset
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arangrhie authored Dec 6, 2022
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Expand Up @@ -83,7 +83,7 @@ Analysis set for using T2T-CHM13v2.0 as a reference for mapping based research i
- [HG002 5mC CpG and other methylation from ONT and HiFi](https://s3-us-west-2.amazonaws.com/human-pangenomics/index.html?prefix=T2T/CHM13/assemblies/annotation/regulation/)

### Variant calls
- [1000 Genomes Project](https://s3-us-west-2.amazonaws.com/human-pangenomics/index.html?prefix=T2T/CHM13/assemblies/variants/1000_Genomes_Project/chm13v2.0/), recalled on the 3,202 samples.
- [1000 Genomes Project](https://s3-us-west-2.amazonaws.com/human-pangenomics/index.html?prefix=T2T/CHM13/assemblies/variants/1000_Genomes_Project/chm13v2.0/), recalled on T2T-CHM13v2.0. Currently available only for chr X and Y, for the entire 3,202 samples or the unrelated 2504 samples.
- [Simons Genome Diversity Project](https://s3-us-west-2.amazonaws.com/human-pangenomics/index.html?prefix=T2T/CHM13/assemblies/variants/SGDP/chm13v2.0/), recalled on T2T-CHM13v2.0.
- [gnomAD v3.1.2](https://ftp.ensembl.org/pub/rapid-release/species/Homo_sapiens/GCA_009914755.4/ensembl/variation/2022_10/vcf/Homo_sapiens-GCA_009914755.4-2022_10-gnomad.vcf.gz) from [FTP](https://ftp.ensembl.org/pub/rapid-release/species/Homo_sapiens/GCA_009914755.4/ensembl/variation/2022_10/vcf/):
This is a lifted over version from GRCh38, annotated with predicted molecular consequence and transcript-specific variant deleteriousness scores from PolyPhen-2 and SIFT using Ensembl Variant Effect Predictor.
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