Filtering quality(phred score) vcf file
Hello, I got some problem with my vcf files
I got a vcf file of an ancient individuals,
and I'd tried to filter the SNPs with the threshold=phred score 30
but, I got a problem
I heard that GQX score is the min(Qual, GQ) but, in this file, Qual, GQ, GQX column had all different values.
The REF allele homogenous sites had only GQX value, not Qual or GQ
so, I thought that I have to filter the SNPs with GQX value,
but, in this file, I do not know what should I do, because the GQX value has different values with the definition
Does anybody have a solution?
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VCF/QUAL is not the same semantics than VCF/FORMAT/GQ
Then, How can I filter the SNPs ? (maybe, in this case, if I set the GQX filter, it makes the REF homogenous sites and the variants sites filtered in different threshold)