wget -O- ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/human_g1k_v37.fasta.gz | \
  gzip -d > human_g1k_v37.fasta
samtools faidx human_g1k_v37.fasta
wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr{{1..22}.phase3_shapeit2_mvncall_integrated_v5a,X.phase3_shapeit2_mvncall_integrated_v1b,Y.phase3_integrated_v2a}.20130502.genotypes.vcf.gz{,.tbi}

for chr in {1..22} X Y; do
  bcftools view --no-version -Ou -c 2 ALL.chr${chr}.phase3*integrated_v[125][ab].20130502.genotypes.vcf.gz | \
  bcftools norm --no-version -Ou -m -any | \
  bcftools norm --no-version -Ob -o ALL.chr${chr}.phase3_integrated.20130502.genotypes.bcf -d none -f human_g1k_v37.fasta && \
  bcftools index -f ALL.chr${chr}.phase3_integrated.20130502.genotypes.bcf
done