gnomad_qc.v4.sample_qc

• assign_ancestry
  • Named Arguments
  • Module Functions
• create_sample_qc_metadata_ht
  • Named Arguments
  • Module Functions
• create_sample_qc_metadata_ht_genomes
  • Named Arguments
  • Module Functions
• generate_qc_mt
  • Named Arguments
  • Module Functions
• hard_filters
  • Named Arguments
  • Hard-filter cutoffs
  • Module Functions
• identify_trios
  • Named Arguments
  • Duplicate identification
  • Pedigree inference
  • Fake Pedigree creation
  • Mendel error calculation
  • Pedigree filtering for final Pedigree generation
  • Create dense trio MT.
  • Module Functions
• interval_qc
  • Named Arguments
  • Sex chromosome interval coverage
  • Compute aggregate interval stats for interval QC
  • Generate interval QC pass annotation
  • Module Functions
• outlier_filtering
  • Named Arguments
  • Apply stratified filtering method.
  • Apply regression filtering method.
  • Determine nearest neighbors for each sample.
  • Apply nearest neighbors filtering method.
  • Create finalized outlier filtering Table.
  • Module Functions
• platform_inference
  • Named Arguments
  • Module Functions
• relatedness
  • Named Arguments
  • Common relatedness estimate arguments
  • cuKING specific relatedness arguments
  • Finalize relatedness specific arguments
  • Compute related samples to drop
  • Module Functions
• sex_inference
  • Named Arguments
  • Determine f-stat sites
  • Sex chromosome interval QC
  • Impute sex ploidy
  • Annotate sex karyotype
  • Module Functions