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URL: https://gatk.broadinstitute.org/hc/en-us/articles/360036350452-VariantFiltration
Proper Citation: GATK VariantFiltration (RRID:SCR_028441)
Description: Software command-line tool designed for hard-filtering variant callsets (VCF files) by applying user-defined criteria to annotate, rather than remove, low-quality variants. It marks fails in the FILTER field (e.g., using JEXL expressions to filter by DP, QD, or FS), making it essential for filtering small datasets, non-model organisms, or whenever Variant Quality Score Recalibration (VQSR) is not feasible
Resource Type: software application, software resource
Keywords: hard-filtering variant callsets, annotate low-quality variants,
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