allele frequency from vcf

Question

[niyomiw88]

I am trying to figure out why the allele frequencies I get from Plink and vcftools are different from what I have on the vcf file. My vcf file was produced by GATK jointgenotyping and filtered using vcftools. I have 448 samples in there. Here is a line from the vcf

DS235882        421     .       T       A       10758.8 .       AC=29;AF=0.186;AN=156;BaseQRankSum=0.394;DP=1264;ExcessHet=0.0000;FS=1.155;InbreedingCoeff=0.6596;MLEAC=32;MLEAF=0.205;MQ=59.92;MQRankSum=0.00;QD=33.41;ReadPosRankSum=0.335;SOR=0.617  GT:AD:DP:GQ:PGT:PID:PL:PS       0/0:22,0:22:60:.:.:0,60,900:.   ./.:0,47:.:99:1|1:405_G_A:2166,147,0:405        ./

I computed the allele frequency using vcftools vcftools --vcf input.vcf --freq2 --out allele_freq --max-alleles 2 and this is what I got;

CHROM   POS N_ALLELES   N_CHR   {FREQ}
DS235882    101 2   140 1   0
DS235882    117 2   148 1   0
DS235882    128 2   150 1   0
DS235882    206 2   160 1   0

I tried plink using plink --vcf input.vcf --freq --allow-extra-chr --out allele_freq

#CHROM  ID  REF ALT ALT_FREQS   OBS_CT
DS235882    .   T   A   0   140
DS235882    .   T   A   0   148
DS235882    .   A   T   0   150
DS235882    .   A   G   0   160

vcftools output gives all 1's and plink gives all 0's. What did I do wrong? Any advice or tips? I even extracted the AF column on my vcf and it looks like this,

DS235882 101 0.012
DS235882 117 0.041
DS235882 128 0.042
DS235882 206 0.012

I want to find out why these analyses wouldn't work. Thanks in advance.

[AMARU]

Hi,

did you figure that out? I have similar issues regarding allele counts. I obtained higher allele counts when samples were processed by GATK3.8 than GATK4.