gnomad.variant_qc.ld

gnomad.variant_qc.ld.get_r_human_readable(...)
gnomad.variant_qc.ld.get_r_for_pair_of_variants(bm, ...)	Get r value (LD) for pair of variants var1 and var2.
gnomad.variant_qc.ld.get_r_within_gene_in_pop(...)	Get LD information (r) for all pairs of variants within gene for a given pop.
gnomad.variant_qc.ld.get_r_within_gene(bm, ...)	Get LD information (r) for all pairs of variants within gene.

gnomad.variant_qc.ld.get_r_human_readable(pop, var1, var2, ref_genome='GRCh37')

Parameters:

• pop (str) –

• var1 (str) –

• var2 (str) –

• ref_genome (str) –

gnomad.variant_qc.ld.get_r_for_pair_of_variants(bm, ld_index, var1, var2)

Get r value (LD) for pair of variants var1 and var2.

bm = get_ld_matrix('nfe')
ld_index = get_ld_index('nfe')
var1 = (hl.parse_locus('1:10146', 'GRCh37'), ['AC', 'A'])
var2 = (hl.parse_locus('1:10151', 'GRCh37'), ['TA', 'T'])
get_r_for_pair_of_variants(bm, ld_index, var1, var2)
# 0.01789767935482124

Parameters:

• bm (BlockMatrix) – Input BlockMatrix

• ld_index (Table) – Corresponding index table

• var1 ((tlocus, tarray)) – Tuple of locus and alleles

• var2 ((tlocus, tarray)) – Tuple of locus and alleles

Returns:

Correlation (r) between two variants

gnomad.variant_qc.ld.get_r_within_gene_in_pop(pop, gene)

Get LD information (r) for all pairs of variants within gene for a given pop.

Warning: this returns a table quadratic in number of variants. Exercise caution with large genes.

Parameters:

• pop (str) – Population for which to get LD information

• gene (str) – Gene symbol as string

Returns:

Table with pairs of variants

gnomad.variant_qc.ld.get_r_within_gene(bm, ld_index, gene, vep_ht=None, reference_genome=None)

Get LD information (r) for all pairs of variants within gene.

Warning: this returns a table quadratic in number of variants. Exercise caution with large genes.

Parameters:

• bm (BlockMatrix) – Input Block Matrix

• ld_index (Table) – Corresponding index table

• gene (str) – Gene symbol as string

• vep_ht (Table) – Table with VEP annotations (if None, gets from get_gnomad_public_data())

• reference_genome (str) – Reference genome to pass to get_gene_intervals for fast filtering to gene

Returns:

Table with pairs of variants