Question

Reference 1000G data

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2.3 years ago

Alexandra ▴ 20

Hi there! I'm looking for a phased vcf file of 1000 Genomes in GRCh38 version. Anyone knows where I can download it? I need this file to perform phasing in BEAGLE 5.4. Thanks,

Beagle phasing vcf 1000G GRCh38 • 1.3k views

ADD COMMENT • link updated 2.3 years ago by Kevin Blighe 88k • written 2.3 years ago by Alexandra ▴ 20

score 0 · Answer 1 · 2022-08-11

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2.3 years ago

Kevin Blighe 88k

Hi,

The phased variant calls for the 1000 Genomes Phase III project for reference genome build GRCh38 in VCF is located here: http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/release/20190312_biallelic_SNV_and_INDEL/

Kevin

ADD COMMENT • link 2.3 years ago by Kevin Blighe 88k

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Thank you!

ADD REPLY • link 2.3 years ago by Alexandra ▴ 20

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No problem - if you're interested, I show how you can do some pre-processing on these in an automated fashion: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2

NB - the tutorial via this link (above) is for the GRCh37 files

ADD REPLY • link 2.3 years ago by Kevin Blighe 88k