Reference 1000G data

Question

[Alexandra]

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,

Answer 1

[Kevin Blighe]

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

[Alexandra]

Thank you!

[Kevin Blighe]

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