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Downstream Filtering

Apply downstream filtering steps to the cleaned VCF to further control the false discovery rate; all steps are optional and users should decide based on the specific purpose of their projects.

Filtering methods include:

  • minGQ - remove variants based on the genotype quality across populations. Note: Trio families are required to build the minGQ filtering model in this step. We provide tables pre-trained with the 1000 genomes samples at different FDR thresholds for projects that lack family structures, and they can be found at the paths below. These tables assume that GQ has a scale of [0,999], so they will not work with newer VCFs where GQ has a scale of [0,99].

    gs://gatk-sv-resources-public/hg38/v0/sv-resources/ref-panel/1KG/v2/mingq/1KGP_2504_and_698_with_GIAB.10perc_fdr.PCRMINUS.minGQ.filter_lookup_table.txt
    gs://gatk-sv-resources-public/hg38/v0/sv-resources/ref-panel/1KG/v2/mingq/1KGP_2504_and_698_with_GIAB.1perc_fdr.PCRMINUS.minGQ.filter_lookup_table.txt
    gs://gatk-sv-resources-public/hg38/v0/sv-resources/ref-panel/1KG/v2/mingq/1KGP_2504_and_698_with_GIAB.5perc_fdr.PCRMINUS.minGQ.filter_lookup_table.txt

  • BatchEffect - remove variants that show significant discrepancies in allele frequencies across batches

  • FilterOutlierSamplesPostMinGQ - remove outlier samples with unusually high or low number of SVs

  • FilterCleanupQualRecalibration - sanitize filter columns and recalibrate variant QUAL scores for easier interpretation