[Vcftools-help] --freq

[Al-Hasani, H. <hoo...@iz...>]

Hello Anthony Marcketta,

could you please explain the reason, why such an error occurs when asking for --freq outcome

"Error: Require Genotypes in VCF file in order to output Frequency Statistics."

the first 5 lines after the header of my vcf file look like:

chr1    4919488 .       G       A       222     .       DP=105;VDB=1.868970e-01;AF1=1;AC1=2;DP4=0,0,50,51;MQ=42;FQ=-282 GT:PL:GQ        1/1:255,255,0:99
chr1    16139332        .       C       T       59      .       DP=25;VDB=1.039870e-01;RPB=3.503245e-01;AF1=0.5;AC1=1;DP4=10,5,2,4;MQ=40;FQ=62;PV4=0.33,0.036,1,0.37    GT:PL:GQ     0/1:89,0,253:92
chr1    22234654        .       C       T       114     .       DP=164;VDB=1.727718e-03;RPB=7.968013e-01;AF1=0.5;AC1=1;DP4=41,75,8,39;MQ=33;FQ=117;PV4=0.024,1,0.033,1  GT:PL:GQ     0/1:144,0,255:99
chr1    22690364        .       G       A       222     .       DP=85;VDB=2.456172e-01;AF1=1;AC1=2;DP4=0,0,58,24;MQ=41;FQ=-271  GT:PL:GQ        1/1:255,244,0:99
chr1    22690383        .       G       A       222     .       DP=133;VDB=4.034246e-01;RPB=1.546991e+00;AF1=1;AC1=2;DP4=1,0,89,41;MQ=41;FQ=-282;PV4=1,1,0.28,1 GT:PL:GQ        1/1:255,255,0:99

I also removed the "chr" just in case but I got the same error...

Could you please help?
Hasani