gnomad.resources.grch37.gnomad

gnomad.resources.grch37.gnomad.public_release(...)

Retrieve publicly released versioned table resource.

gnomad.resources.grch37.gnomad.coverage(...)

Retrieve gnomAD's coverage table by data_type.

gnomad.resources.grch37.gnomad.liftover(...)

Get the 38 liftover of gnomad v2.1.1.

gnomad.resources.grch37.gnomad.public_pca_loadings([...])

Return the TableResource containing sites and loadings from genetic ancestry PCA.

gnomad.resources.grch37.gnomad.release_vcf_path(...)

Publically released VCF.

gnomad.resources.grch37.gnomad.pext([pext_type])

Retrieve proportion expressed across transcripts (pext) data.

gnomad.resources.grch37.gnomad.constraint()

Retrieve gene constraint table.

gnomad.resources.grch37.gnomad.mnv([distance])

Retrieve multinucleotide variant table.

gnomad.resources.grch37.gnomad.browser_gene()

Retrieve browser gene table.
gnomad.resources.grch37.gnomad.public_release(data_type)[source]

Retrieve publicly released versioned table resource.

Parameters:

data_type (str) – One of “exomes” or “genomes”

Return type:

VersionedTableResource

Returns:

Release Table

gnomad.resources.grch37.gnomad.coverage(data_type)[source]

Retrieve gnomAD’s coverage table by data_type.

Parameters:

data_type (str) – One of “exomes” or “genomes”

Return type:

VersionedTableResource

Returns:

Coverage Table

gnomad.resources.grch37.gnomad.liftover(data_type)[source]

Get the 38 liftover of gnomad v2.1.1.

Parameters:

data_type (str) – One of “exomes” or “genomes”

Return type:

VersionedTableResource

Returns:

Release Table

gnomad.resources.grch37.gnomad.public_pca_loadings(subgrp='')[source]

Return the TableResource containing sites and loadings from genetic ancestry PCA.

Parameters:

subgrp (str) – Can be empty (“”) -> global, “eas” or “nfe”

Return type:

GnomadPublicTableResource

Returns:

gnomAD public PCA loadings TableResource

gnomad.resources.grch37.gnomad.release_vcf_path(data_type, version, contig)[source]

Publically released VCF. Provide specific contig, i.e. “20”, to retrieve contig specific VCF.

Parameters:

  • data_type (str) – One of “exomes” or “genomes”

  • version (str) – One of the release versions of gnomAD on GRCh37

  • contig (str) – Single contig “1” to “Y”

Return type:

str

Returns:

Path to VCF

gnomad.resources.grch37.gnomad.pext(pext_type='base_level')[source]

Retrieve proportion expressed across transcripts (pext) data.

Parameters:

pext_type (str) – One of “annotation_level” or “base_level”. Default is “base_level”.

Return type:

GnomadPublicTableResource

Returns:

Pext Table.

gnomad.resources.grch37.gnomad.constraint()[source]

Retrieve gene constraint table.

Return type:

GnomadPublicTableResource

Returns:

Gene constraint Table.

gnomad.resources.grch37.gnomad.mnv(distance=1)[source]

Retrieve multinucleotide variant table.

Parameters:

distance (int) – Distance between two SNVs in MNV. Default is 1.

Return type:

GnomadPublicTableResource

Returns:

MNV Table.

gnomad.resources.grch37.gnomad.browser_gene()[source]

Retrieve browser gene table.

Return type:

GnomadPublicTableResource

Returns:

Browser gene Table.