BGE Toolkit

Contents:

  • Command-Line Interface
    • bge-toolkit
    • bge-toolkit qc
    • bge-toolkit qc concordance
      • Aggregations
        • Grouping
        • Aggregation
      • Notes
      • Examples
    • bge-toolkit qc sample-qc
      • Examples
      • Notes
  • Python API Reference
    • bge_toolkit.qc
      • Concordance Reference
        • JointCallSet
          • JointCallSet
        • JoinType
          • JoinType
        • Selectors
          • ALL_GROUP
          • ALL_AGG
        • Concordance
          • concordance()
        • ConcordanceTable
          • ConcordanceTable
        • ConcordanceView
          • ConcordanceView
        • Statistic
          • Statistic
          • bge_toolkit.common
        • Binning Functions
          • mac_bin()
          • maf_bin()
          • gq_bin()
          • dp_bin()
          • max_gp_bin()
          • qual_approx_bin()
          • info_score_bin()
      • Sample QC Reference
        • sample_qc
          • sample_qc()
        • High Level Functions
          • select_high_quality_common_sites()
          • infer_ancestry()
          • calculate_sample_qc_stats()
        • Lower Level Functions
          • filter_to_high_quality_exome_intervals()
          • filter_contamination_rate()
          • filter_chimeric_reads()
          • filter_genotypes()
          • filter_to_high_quality_common_sites()
          • compute_pcs()
          • estimate_call_rate_through_gq_stats()
          • impute_and_check_sex()
          • identify_outliers_in_qc_stats()
        • SampleQCResult
          • SampleQCResult
BGE Toolkit
  • Search

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