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Variants estimated by gatk4 mutect2 are dramatically less compared estimated by vardict or others.
Dear GATK team.
Hello. I'm GATK4 user.
I compared the number of variants between gatk4 mutect2 raw variants and Vardict raw variants. As compared between output of callers, I identified they are so different.
I have two questions.
Through this document ( https://software.broadinstitute.org/gatk/documentation/article?id=11136) and @Sheila 's comment, I understood that gnomAD and PON are not effect on the number of variants and that these two database (gnomAD and PON) are only used for annotation. (Q1. Is it okay?)
Q2. Then, could I think that different number of variants between mutect2 and other callers depend only on difference of caller's calling method?