search

AstraZeneca-NGS / VarDictJava

VarDict Java port
MIT License
127 stars 55 forks source link

Is it possible to filter orientation bias? #361

Closed kimjr89 closed 2 years ago

kimjr89 commented 2 years ago

image

VCF files generated by VarDict don't seem to have an orientation bias(different from strand bias) filter which is supported by Mutect2.

Since I'm working on a project dealing with very low-frequency alleles, false-positive from oxoG should be filtered.

Does VarDict support an orientation bias filter? Or are there any other methods like piping other tools to enable the filtering?

Thanks.

PolinaBevad commented 2 years ago

Hi @kimjr89, Sorry, we do not support orientation bias filtering at the moment. I know that GATK has some additional tools on filtering Orientation Bias on top of Mutect2 calls, maybe you can check if this will work for VarDict results as well?