Index

A

ad (hail.representation.Genotype attribute) aggregate_by_key() (hail.KeyTable method) (hail.VariantDataset method) allele() (hail.representation.Variant method) alt (hail.representation.AltAllele attribute) alt() (hail.representation.Variant method) alt_allele() (hail.representation.Variant method) alt_alleles (hail.representation.Variant attribute) AltAllele (class in hail.representation) annotate() (hail.KeyTable method)

annotate_alleles_expr() (hail.VariantDataset method) annotate_genotypes_expr() (hail.VariantDataset method) annotate_global() (hail.VariantDataset method) annotate_global_expr() (hail.VariantDataset method) annotate_samples_expr() (hail.VariantDataset method) annotate_samples_table() (hail.VariantDataset method) annotate_variants_db() (hail.VariantDataset method) annotate_variants_expr() (hail.VariantDataset method) annotate_variants_table() (hail.VariantDataset method) annotate_variants_vds() (hail.VariantDataset method)

B

balding_nichols_model() (hail.HailContext method)

C

cache() (hail.KeyTable method) (hail.VariantDataset method) Call (class in hail.representation) category() (hail.representation.AltAllele method) colkey_schema (hail.VariantDataset attribute) collect() (hail.KeyTable method) columns (hail.KeyTable attribute)

complete_trios() (hail.representation.Pedigree method) concordance() (hail.VariantDataset method) contains() (hail.representation.Interval method) contig (hail.representation.Locus attribute) (hail.representation.Variant attribute) count() (hail.KeyTable method) (hail.VariantDataset method) count_variants() (hail.VariantDataset method)

D

deduplicate() (hail.VariantDataset method) delete_va_attribute() (hail.VariantDataset method) dosage() (hail.representation.Genotype method)

dp (hail.representation.Genotype attribute) drop() (hail.KeyTable method) drop_samples() (hail.VariantDataset method) drop_variants() (hail.VariantDataset method)

E

end (hail.representation.Interval attribute) eval_expr() (hail.HailContext method) eval_expr_typed() (hail.HailContext method) exists() (hail.KeyTable method) expand_types() (hail.KeyTable method) explode() (hail.KeyTable method) export() (hail.KeyTable method) (hail.LDMatrix method) export_cassandra() (hail.KeyTable method) export_elasticsearch() (hail.KeyTable method) export_gcta_grm() (hail.KinshipMatrix method)

export_gcta_grm_bin() (hail.KinshipMatrix method) export_gen() (hail.VariantDataset method) export_genotypes() (hail.VariantDataset method) export_id_file() (hail.KinshipMatrix method) export_mongodb() (hail.KeyTable method) export_plink() (hail.VariantDataset method) export_rel() (hail.KinshipMatrix method) export_samples() (hail.VariantDataset method) export_solr() (hail.KeyTable method) export_tsv() (hail.KinshipMatrix method) export_variants() (hail.VariantDataset method) export_vcf() (hail.VariantDataset method)

F

fam (hail.representation.Trio attribute) father (hail.representation.Trio attribute) Field (class in hail.expr) file_version() (hail.VariantDataset method) filter() (hail.KeyTable method) filter_alleles() (hail.VariantDataset method) filter_genotypes() (hail.VariantDataset method) filter_intervals() (hail.VariantDataset method) filter_multi() (hail.VariantDataset method) filter_samples_expr() (hail.VariantDataset method) filter_samples_list() (hail.VariantDataset method)

filter_samples_table() (hail.VariantDataset method) filter_to() (hail.representation.Pedigree method) filter_variants_expr() (hail.VariantDataset method) filter_variants_list() (hail.VariantDataset method) filter_variants_table() (hail.VariantDataset method) flatten() (hail.KeyTable method) forall() (hail.KeyTable method) fraction_reads_ref() (hail.representation.Genotype method) from_dataframe() (hail.KeyTable static method) from_pandas() (hail.KeyTable static method) from_py() (hail.KeyTable static method) from_table() (hail.VariantDataset static method)

G

Genotype (class in hail.representation) genotype_schema (hail.VariantDataset attribute) genotypes_table() (hail.VariantDataset method) get() (hail.representation.Struct method) get_running() (hail.HailContext static method) global_schema (hail.VariantDataset attribute)

globals (hail.VariantDataset attribute) gp (hail.representation.Genotype attribute) gq (hail.representation.Genotype attribute) grep() (hail.HailContext method) grm() (hail.VariantDataset method) gt (hail.representation.Call attribute) (hail.representation.Genotype attribute)

H

hadoop_copy() (in module hail.utils) hadoop_read() (in module hail.utils)

hadoop_write() (in module hail.utils) HailContext (class in hail) hardcalls() (hail.VariantDataset method)

I

ibd() (hail.VariantDataset method) ibd_prune() (hail.VariantDataset method) import_bed() (hail.KeyTable static method) import_bgen() (hail.HailContext method) import_fam() (hail.KeyTable static method) import_gen() (hail.HailContext method) import_interval_list() (hail.KeyTable static method) import_plink() (hail.HailContext method) import_table() (hail.HailContext method) import_vcf() (hail.HailContext method) impute_sex() (hail.VariantDataset method) in_X_non_PAR() (hail.representation.Variant method) in_X_PAR() (hail.representation.Variant method) in_Y_non_PAR() (hail.representation.Variant method) in_Y_PAR() (hail.representation.Variant method) index_bgen() (hail.HailContext method) indexed() (hail.KeyTable method) Interval (class in hail.representation) is_autosomal() (hail.representation.Variant method) is_autosomal_or_pseudoautosomal() (hail.representation.Variant method) is_biallelic() (hail.representation.Variant method) is_called() (hail.representation.Call method) (hail.representation.Genotype method) is_called_non_ref() (hail.representation.Call method) (hail.representation.Genotype method)

is_complete() (hail.representation.Trio method) is_complex() (hail.representation.AltAllele method) is_deletion() (hail.representation.AltAllele method) is_female (hail.representation.Trio attribute) is_het() (hail.representation.Call method) (hail.representation.Genotype method) is_het_non_ref() (hail.representation.Call method) (hail.representation.Genotype method) is_het_ref() (hail.representation.Call method) (hail.representation.Genotype method) is_hom_ref() (hail.representation.Call method) (hail.representation.Genotype method) is_hom_var() (hail.representation.Call method) (hail.representation.Genotype method) is_indel() (hail.representation.AltAllele method) is_insertion() (hail.representation.AltAllele method) is_male (hail.representation.Trio attribute) is_mitochondrial() (hail.representation.Variant method) is_MNP() (hail.representation.AltAllele method) is_not_called() (hail.representation.Call method) (hail.representation.Genotype method) is_SNP() (hail.representation.AltAllele method) is_transition() (hail.representation.AltAllele method) is_transversion() (hail.representation.AltAllele method)

J

join() (hail.KeyTable method) (hail.VariantDataset method)

K

key (hail.KeyTable attribute) key_by() (hail.KeyTable method)

key_schema (hail.KinshipMatrix attribute) KeyTable (class in hail) KinshipMatrix (class in hail)

L

ld_matrix() (hail.VariantDataset method) ld_prune() (hail.VariantDataset method) LDMatrix (class in hail) linreg() (hail.VariantDataset method) linreg3() (hail.VariantDataset method) linreg_burden() (hail.VariantDataset method)

linreg_multi_pheno() (hail.VariantDataset method) lmmreg() (hail.VariantDataset method) Locus (class in hail.representation) locus() (hail.representation.Variant method) logreg() (hail.VariantDataset method) logreg_burden() (hail.VariantDataset method)

M

make_table() (hail.VariantDataset method) matrix() (hail.KinshipMatrix method) (hail.LDMatrix method)

maximal_independent_set() (hail.KeyTable method) mendel_errors() (hail.VariantDataset method) min_rep() (hail.VariantDataset method) mother (hail.representation.Trio attribute)

N

naive_coalesce() (hail.VariantDataset method) num_alleles() (hail.representation.Variant method) num_alt_alleles() (hail.representation.Call method) (hail.representation.Genotype method) (hail.representation.Variant method)

num_columns (hail.KeyTable attribute) num_genotypes() (hail.representation.Variant method) num_mismatch() (hail.representation.AltAllele method) num_partitions() (hail.KeyTable method) (hail.VariantDataset method) num_samples (hail.VariantDataset attribute)

O

od() (hail.representation.Genotype method) one_hot_alleles() (hail.representation.Call method) (hail.representation.Genotype method)

one_hot_genotype() (hail.representation.Call method) (hail.representation.Genotype method) order_by() (hail.KeyTable method) overlaps() (hail.representation.Interval method)

P

p_ab() (hail.representation.Genotype method) parse() (hail.representation.Interval static method) (hail.representation.Locus static method) (hail.representation.Variant static method) pc_relate() (hail.VariantDataset method) pca() (hail.VariantDataset method)

Pedigree (class in hail.representation) persist() (hail.KeyTable method) (hail.VariantDataset method) pl (hail.representation.Genotype attribute) position (hail.representation.Locus attribute) pretty() (hail.expr.Type method) proband (hail.representation.Trio attribute)

Q

query() (hail.KeyTable method) query_genotypes() (hail.VariantDataset method) query_genotypes_typed() (hail.VariantDataset method) query_samples() (hail.VariantDataset method)

query_samples_typed() (hail.VariantDataset method) query_typed() (hail.KeyTable method) query_variants() (hail.VariantDataset method) query_variants_typed() (hail.VariantDataset method)

R

range() (hail.KeyTable static method) read() (hail.HailContext method) (hail.LDMatrix static method) (hail.representation.Pedigree static method) read_table() (hail.HailContext method) ref (hail.representation.AltAllele attribute) (hail.representation.Variant attribute)

rename() (hail.KeyTable method) rename_samples() (hail.VariantDataset method) repartition() (hail.KeyTable method) (hail.VariantDataset method) report() (hail.HailContext method) (hail.utils.Summary method) rowkey_schema (hail.VariantDataset attribute) rrm() (hail.VariantDataset method)

S

same() (hail.KeyTable method) (hail.VariantDataset method) sample_annotations (hail.VariantDataset attribute) sample_ids (hail.VariantDataset attribute) sample_list() (hail.KinshipMatrix method) sample_qc() (hail.VariantDataset method) sample_schema (hail.VariantDataset attribute) sample_variants() (hail.VariantDataset method) samples_table() (hail.VariantDataset method) schema (hail.KeyTable attribute) select() (hail.KeyTable method)

set_va_attributes() (hail.VariantDataset method) show() (hail.KeyTable method) split_multi() (hail.VariantDataset method) start (hail.representation.Interval attribute) (hail.representation.Variant attribute) stop() (hail.HailContext method) storage_level() (hail.VariantDataset method) stripped_snp() (hail.representation.AltAllele method) Struct (class in hail.representation) summarize() (hail.VariantDataset method) Summary (class in hail.utils)

T

take() (hail.KeyTable method) TAltAllele (class in hail.expr) TArray (class in hail.expr) TBoolean (class in hail.expr) TCall (class in hail.expr) TDict (class in hail.expr) TDouble (class in hail.expr) tdt() (hail.VariantDataset method) TFloat (class in hail.expr) TGenotype (class in hail.expr) TInt (class in hail.expr) TInterval (class in hail.expr)

TLocus (class in hail.expr) TLong (class in hail.expr) to_dataframe() (hail.KeyTable method) to_local_matrix() (hail.LDMatrix method) to_pandas() (hail.KeyTable method) transitive_fields() (hail.expr.TStruct method) Trio (class in hail.representation) trios (hail.representation.Pedigree attribute) TSet (class in hail.expr) TString (class in hail.expr) TStruct (class in hail.expr) TVariant (class in hail.expr) Type (class in hail.expr)

U

union() (hail.KeyTable method) (hail.VariantDataset method)

unpersist() (hail.KeyTable method) (hail.VariantDataset method)

V

Variant (class in hail.representation) variant_list() (hail.LDMatrix method) variant_qc() (hail.VariantDataset method) variant_schema (hail.VariantDataset attribute)

VariantDataset (class in hail) variants_table() (hail.VariantDataset method) vep() (hail.VariantDataset method) version (hail.HailContext attribute)

W

was_split() (hail.VariantDataset method) write() (hail.KeyTable method) (hail.LDMatrix method) (hail.VariantDataset method) (hail.representation.Pedigree method)

write_partitioning() (hail.HailContext method)