Sorry if this might be a trivial question!

I read a lot about this until I got lost. I need to download wgs VCF file from the 1000 genomes ftp site. I need the snps (snvs and indels), most importantly, I need to have the individual genotypes of all the persons involved.

so for example, this file :

 [ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz][1] 

which was referenced many times on biostars, does not contain individual genotypes. I need something similar to what [those files][2] contain. Is there one global file containing snps/indels for wgs data including genotypes of the various samples ?

thanks!


  [1]: http://%20ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz
  [2]: ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/phase1/analysis_results/integrated_call_sets/

You can download the entire data per chromosome (chr1-22 & chrX) —including individual genotypes for both indels and SNPs— using this code:

    prefix="ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr" ;
    
    suffix=".phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz" ;
    
    for chr in {1..22} X; do
        wget $prefix$chr$suffix $prefix$chr$suffix.tbi ;
    done

From: https://www.biostars.org/p/271694/

Kevin