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AstraZeneca-NGS / VarDictJava

VarDict Java port
MIT License
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Allele frequency parameter in VarDictJava #366

Closed ds21uab closed 2 years ago

ds21uab commented 2 years ago

Hi,

I am trying to understand the -f parameter in VarDictJava. As it states it is the allele frequency (AF). So I was wondering which population database for example GnomAD VarDict is using to get the AF values? Or -f is the variant allele fraction?

PolinaBevad commented 2 years ago

Hi @ds21uab, It is variant allele fraction threshold (calculated as VD/DP), you can see the options here: https://github.com/AstraZeneca-NGS/VarDictJava#vardictjava-options . So if the variant AF exceeds this threshold, we will keep it in the filtered results in VCF. We do not use gnomAD in VarDict, but you can annotate VCF using SnpEff/vcfanno to get gnomAD AF.