EUR_AF>0.05 from 1000G release with 1029 genomes

#1. download 

$wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/integrated_call_sets/ALL.wgs.integrated_phase1_v3.20101123.snps_indels_sv.sites.vcf.gz

#2. unzip

$gunzip ALL.wgs.integrated_phase1_v3.20101123.snps_indels_sv.sites.vcf.gz

#3. size?

$wc -l ALL.wgs.integrated_phase1_v3.20101123.snps_indels_sv.sites.vcf.gz

39706744 


#4. Get the variants whose AF>=0.05 in EUR population

$grep -o ".*EUR_AF=\([0-1]\.[0-9]*\)" ALL.wgs.integrated_phase1_v3.20101123.snps_indels_sv.sites.vcf | awk -F'EUR_AF=' '{if ($NF >= 0.05) print}' > body.vcf

#5. Header

$head -n 100 ALL.wgs.integrated_phase1_v3.20101123.snps_indels_sv.sites.vcf | grep '^#'
> head.txt

#6. cat

$cat head.txt body.vcf > 1000g.wgs.integrated_phase1_v3.20101123.snps_indels_sv.sites.EUR_AF_0.05.vcf