Hi,Sorry to ask basic.
I get such vcf by smtools mpileup, But can't understand it.
scaffold_1 8463589 . T C 47 . DP=5;VDB=0.0520;AF1=0.500;AFE=0.500;DP4=0,0,3,2;MQ=38 PL:GT:GQ 92,15,92:0/1:77
The ref is T, all my 5 reads are C at this site. So how the AF1 (site allele frequency of the strongest non-reference allele) is 0.5 ?
How samtools computes AF1?
PS: I didn't find any explain about AFE. what is it?
Thanks!
I get such vcf by smtools mpileup, But can't understand it.
scaffold_1 8463589 . T C 47 . DP=5;VDB=0.0520;AF1=0.500;AFE=0.500;DP4=0,0,3,2;MQ=38 PL:GT:GQ 92,15,92:0/1:77
The ref is T, all my 5 reads are C at this site. So how the AF1 (site allele frequency of the strongest non-reference allele) is 0.5 ?
How samtools computes AF1?
PS: I didn't find any explain about AFE. what is it?
Thanks!
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