GATK pipeline AF and GT fields in annovar
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8 weeks ago
Edmond • 0


I have created a pipeline following the best practices of GATK.

After that I have annotated the vcf fields with ANNOVAR, using the command

So fat so good until I checked the output, here it is the two columns belonging to AF and GT

GT and AF fields

As you can see I have a distribution of AF values and the genotype in letters. All I want to know if the variant is homocigotus or heterocygotus (sorry I dont know how it is spelled)

Furhtermore is any DB that gives us the inheritance mode? i.e dominant or recessive ?

wes-seq gatk annovar • 134 views

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