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 population PCA.

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

Publically released VCF.
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(subpop='')[source]

Return the TableResource containing sites and loadings from population PCA.

Parameters:

subpop (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