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From: Al-Hasani, H. <hoo...@iz...> - 2014-05-22 14:26:37
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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 |