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VariantFiltration for genotype calls (rather than variant calls)
I wanted to use VariantFiltration/-G_filter/-G_filterName to filter some low quality genotype calls. With VariantFiltration (http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_filters_VariantFiltration.html) I can use JEXL expressions (http://www.broadinstitute.org/gatk/guide/article?id=1255) to filter bad genotpe calls. For example I can use JEXL expression "DP<10" to filter calls in regions where coverage is too low. However, this only achieves adding a tag to the genotype calls. What I would really want is to set those genotype calls to missing (i.e. ./.), but I don't see an option to do so in the Walker. It seems like a missing feature.
Or maybe there are other ways to get what I need? Again, I don't want to filter the variant, only the genotypes.