where to find GRCh38 for 1000 Genomes

Question

[raalsuwaidi]

Hi,

in the previous GRCh37 build from 1000Genomes files were available in vcf format by chromosome through their portal. now for the GRCh38 i cannot seem to find the files.

any help on where i can find the files?

Answer 1

[4galaxy77]

Genotypes can be found here http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20201028_3202_raw_GT_with_annot/

Phased haplotypes can be found http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20201028_3202_phased/

[raalsuwaidi]

thank you so much. would it be possible if you can point me to where i can fine the map file? i will need it to be used in the imputation process.

Answer 2

[chrchang523]

A plink2-formatted version of the current GRCh38 1000 Genomes phase 3 callset, preserving all annotations and phase information, is now available at https://www.cog-genomics.org/plink/2.0/resources . (Note that you can use --export vcf bgz to generate VCFs from this.)