perl /home/[user]/calculate_allele_frq_from_vcf.pl \
-vcf /home/[user]/share/1000genomesPhase3VCFFiles/ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz \
-sample_panel /home/[user]/share/1000genomesPhase3VCFFiles/integrated_call_samples_v3.20130502.ALL.panel \
-out_dir /home/[user]/Desktop/AlleleFrequency \
-tabix  /home/[user]/tabix-0.2.6 \
-vcftools_dir /home/[user]/vcftools_0.1.13 \
-region 1:1-10000 \
-pop CEU,FIN \