BGE Toolkit

Installation

$ git clone https://github.com/atgu/bge-toolkit.git
$ cd bge-toolkit
$ pip3 install .

Documentation

This is the documentation for both the Python API and the CLI for the 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
          • JointCallSet.close()
          • JointCallSet.full_outer_join()
          • JointCallSet.global_concordance()
          • JointCallSet.n_sample_overlaps
          • JointCallSet.n_variant_overlaps
          • JointCallSet.sample_concordance()
          • JointCallSet.sample_overlaps()
          • JointCallSet.variant_concordance()
          • JointCallSet.variant_overlaps()
      • JoinType
        • JoinType
          • JoinType.outer
          • JoinType.inner
      • Selectors
        • ALL_GROUP
        • ALL_AGG
      • Concordance
        • concordance()
      • ConcordanceTable
        • ConcordanceTable
          • ConcordanceTable.agg_vars()
          • ConcordanceTable.close()
          • ConcordanceTable.get_view()
          • ConcordanceTable.group_vars()
          • ConcordanceTable.load()
          • ConcordanceTable.write()
      • ConcordanceView
        • ConcordanceView
          • ConcordanceView.export()
          • ConcordanceView.export_all()
          • ConcordanceView.fields
          • ConcordanceView.plot()
          • ConcordanceView.plot_all()
          • ConcordanceView.result()
      • Statistic
        • Statistic
          • Statistic.nonref_concordance_rate
          • Statistic.concordance_rate
          • Statistic.f1_score
        • 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
          • SampleQCResult.ancestry_pop
          • SampleQCResult.chimera_reads
          • SampleQCResult.close()
          • SampleQCResult.contamination
          • SampleQCResult.export()
          • SampleQCResult.filter_to()
          • SampleQCResult.gq_fraction
          • SampleQCResult.load()
          • SampleQCResult.passing_samples()
          • SampleQCResult.pcs
          • SampleQCResult.plot_chimera_reads()
          • SampleQCResult.plot_gq_fraction_density()
          • SampleQCResult.plot_pcs()
          • SampleQCResult.plot_qc_metric_boxplots()
          • SampleQCResult.plot_qc_metric_density()
          • SampleQCResult.qc_metrics
          • SampleQCResult.sample_id
          • SampleQCResult.sex_info
          • SampleQCResult.table
          • SampleQCResult.write()

Indices and tables

• Index

• Module Index

• Search Page