Downloading 1000genome phase 3 data in 38 build

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3.1 years ago

AVA ▴ 40

I am new to the field of genomics. I would like to perform a PCA using 1K data. My data is in 38 build and therefore, I would like to download 1K phase 3 data in 38 build from the site below:

http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/supporting/GRCh38_positions/

I have no clue how I can download files for all chromosomes using one command because merged data is not available in 38 build (as for build 37 ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20100804/ALL.2of4intersection.20100804.genotypes.vcf.gz) or I have missed it.

1000genomes • 1.7k views

ADD COMMENT • link updated 13 months ago by Ram 43k • written 3.1 years ago by AVA ▴ 40

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I download from ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/release/20190312_biallelic_SNV_and_INDEL/
a few months ago, but it's 404 now?

ADD REPLY • link 3.1 years ago by MatthewP ★ 1.4k

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I'm not sure if it will help you but I used the gatk bundle for this.You can access here

ADD REPLY • link 2.8 years ago by enes ▴ 40

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