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Test-drive the GATK tools and Best Practices pipelines on Terra
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Drop filtered variants VariantFiltration
I am using GATK VariantFiltration tool to do some hardfiltering of variants and it works fine. However, the total variants remain same before and after filtering by marking the variants "PASS" that pass the filter. I explored through the documentation and forum to find out if there is a way to drop the variants from the file that do not meet the filtering criteria but couldn't find. Could someone give any suggestions to fix this.