#64 using VCFtool MAF calculation

[Sudhir S Jadhao]

Dear Sir/Ma'am,

I am using VCFtools to analyse population genomics data.

I have a vcf file containing 60 samples.

To calculate allele frequency using VCFtools, I am using below command:

vcftools --vcf input.vcf --freq --out allelefreq

output:
CHROM POS N_ALLELES N_CHR {ALLELE:FREQ}
chr1 10146 2 2 AC:0.5 A:0.5
chr1 10150 2 0 C:-nan T:-nan

I have a few questions about output:
1) The allele frequency I am getting for a particular position is with respect to all 60 samples?
2) Is it Minor allele frequency for my population?
3) If it is not Minor allele frequency for my population, can you please tell me how Can I calculate Minor allele frequency for my population using VCFtools.

Thank you In advance for your help