Dear Sir,
I used samtools to create VCF files. There are some questions about VCF
file.
I listed some data of my vcf file as follows:
chr7 61969324 . G C,T 176 .
DP=9965;VDB=2.727029e-04;RPB=5.785173e-01;AF1=1;AC1=2;DP4=10,2,9097,560;MQ=18;FQ=-282;PV4=0.15,1.1e-86,0.00045,1
GT:PL:GQ 1/1:209,255,0,214,255,208:99
chr7 61969379 . G T 122 .
DP=9801;VDB=8.406953e-02;RPB=-3.731877e-01;AF1=1;AC1=2;DP4=5,0,8729,353;MQ=13;FQ=-282;PV4=1,0.03,0.002,1
GT:PL:GQ 1/1:155,255,0:99
chr9 68414372 . A G 220 .
DP=733;VDB=3.128635e-01;RPB=-1.010502e-01;AF1=0.5;AC1=1;DP4=206,37,303,106;MQ=20;FQ=107;PV4=0.0017,0.011,1,0.19
GT:PL:GQ 0/1:250,0,134:99
chr9 68415852 . T C 110 .
DP=699;VDB=4.876058e-01;RPB=-3.048264e-02;AF1=0.5;AC1=1;DP4=60,53,86,99;MQ=28;FQ=113;PV4=0.28,2.2e-34,1,1
GT:PL:GQ 0/1:140,0,184:99
1. How do I get "Allele frequency" from VCF? I viewed the information in
"header". "AF1" and "AC1" are related "Allele frequency".
In the first row of my vcf file, the "ALT" has two types (C,T). How do I
obtain the "Allele frequency" of them respectively?
2. In the second row of my vcf file, the value of "AF1" is 1. So, it means
there are 9801 sequences belonging to "ALT". Am I right?
Thank you for kind help.
Best Regards,
Wei-Chi Wang
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