vcf.split

cloud.vcf.split

Split samples from multi-sample VCF.

Functions

Name	Description
ls_samples	List samples in an aggregate VCF.
split_one_sample	Split one sample from multi-sample VCF.
split_vcf	Split individual sample VCFs from an aggreate VCF.

ls_samples

cloud.vcf.split.ls_samples(vcf_uri, config=None)

List samples in an aggregate VCF.

Parameters

Name	Type	Description	Default
vcf_uri	str	S3 path to aggregate VCF.	required
config	Optional[Mapping[str, str]]	TileDB config params.	None

Returns

Name	Type	Description
	list[str]	Samples included in VCF.

split_one_sample

cloud.vcf.split.split_one_sample(vcf_uri, sample, output_uri, config=None)

Split one sample from multi-sample VCF.

Parameters

Name	Type	Description	Default
vcf_uri	str	URI of VCF to isolate from.	required
sample	str	Sample name to isolate.	required
output_uri	str	URI to deposit isolated VCF.	required
config	Optional[Mapping[str, str]]	TileDB config object.	None

Returns

Name	Type	Description
	str	URI of isolated sample.

split_vcf

cloud.vcf.split.split_vcf(
    vcf_uri
    output_uri
    namespace
    acn
    resources={'cpu': '2', 'memory': '30Gi'}
    compute=True
    verbose=False
    samples=None
    retry_count=1
    max_workers=100
    config=None
)

Split individual sample VCFs from an aggreate VCF.

Given an aggregate VCF file containing multiple samples, split all samples into isolated VCFs, one per sample. Alternatively, specify sample(s) to split apart from VCF if not all isolated VCFs are needed.

Parameters

Name	Type	Description	Default
vcf_uri	str	Aggregate VCF URI.	required
output_uri	str	Output URI to write isolated VCFs.	required
namespace	str	TileDB Cloud namespace to process task graph.	required
acn	str	Access credential friendly name to auth storage i/o.	required
resources	Mapping[str, str]	Resources applied to splitting UDF (start with default).	{'cpu': '2', 'memory': '30Gi'}
compute	bool	Whether to execute DAG.	True
verbose	bool	Logging verbosity.	False
samples	Optional[Sequence[str]]	Indicate a batch of sample names within vcf_uri to isolate if it is undesired to isolate all samples (default).	None
retry_count	int	Number of Node retries.	1
max_workers	int	Max workers to engage simultaneously.	100
config	Optional[Mapping[str, int]]	TileDB configuration parameters used to configure virtual filesystem handler.	None

Returns

Name	Type	Description
	DAG	DAG instantiated as specified.