gnomad_qc.v5.variant_qc.import_variant_qc_vcf

Script to load variant QC result VCF into a Hail Table.

usage: gnomad_qc.v5.variant_qc.import_variant_qc_vcf.py [-h] [-o] [--test]
                                                        [--environment {rwb,batch,dataproc}]
                                                        [--app-name APP_NAME]
                                                        [--driver-cores DRIVER_CORES]
                                                        [--driver-memory DRIVER_MEMORY]
                                                        [--worker-cores WORKER_CORES]
                                                        [--worker-memory WORKER_MEMORY]
                                                        --vcf-path VCF_PATH
                                                        --model-id MODEL_ID
                                                        [--n-partitions N_PARTITIONS]
                                                        [--header-path HEADER_PATH]
                                                        [--array-elements-required]
                                                        [--is-split]
                                                        [--deduplication-check]
                                                        [--snp-features SNP_FEATURES [SNP_FEATURES ...]]
                                                        [--indel-features INDEL_FEATURES [INDEL_FEATURES ...]]

Named Arguments

-o, --overwrite

Whether to overwrite data already present in the output Table.

Default: False

--test

Whether to use a tmp path for output.

Default: False

--environment

Possible choices: rwb, batch, dataproc

Compute environment.

Default: “batch”

--app-name

Job name for the batch/QoB backend.

--driver-cores

Number of driver cores (Batch only).

--driver-memory

Driver memory (Batch only).

--worker-cores

Number of worker cores (Batch only).

--worker-memory

Worker memory (Batch only).

--vcf-path

Path to variant QC result VCF. Can be Hadoop glob patterns.

--model-id

Model ID for the result HT.

--n-partitions

Number of partitions for the output Table.

Default: 5000

--header-path

Optional header file to use for import.

--array-elements-required

Set array_elements_required=True in import_vcf.

Default: False

--is-split

Whether the VCF is already split.

Default: False

--deduplication-check

Remove duplicate variants (for overlapping shards).

Default: False

--snp-features

SNP model features (stored as a global).

Default: [‘AS_QD’, ‘AS_pab_max’, ‘AS_MQRankSum’, ‘AS_ReadPosRankSum’, ‘AS_FS’, ‘AS_SOR’, ‘AS_MQ’]

--indel-features

Indel model features (stored as a global).

Default: [‘AS_QD’, ‘AS_pab_max’, ‘AS_MQRankSum’, ‘AS_ReadPosRankSum’, ‘AS_FS’, ‘AS_SOR’]

Module Functions

gnomad_qc.v5.variant_qc.import_variant_qc_vcf.import_variant_qc_vcf(...)	Import variant QC result sites VCF into a HT.
gnomad_qc.v5.variant_qc.import_variant_qc_vcf.main(args)	Load a single variant QC result VCF into a Hail Table.
gnomad_qc.v5.variant_qc.import_variant_qc_vcf.get_script_argument_parser()	Get script argument parser.

Script to load variant QC result VCF into a Hail Table.

gnomad_qc.v5.variant_qc.import_variant_qc_vcf.import_variant_qc_vcf(vcf_path, model_id, num_partitions=5000, import_header_path=None, array_elements_required=False, is_split=False, deduplicate_check=False)

Import variant QC result sites VCF into a HT.

Parameters:

• vcf_path (Union[str, List[str]]) – Path(s) to variant QC result sites VCF(s). Can be a Hadoop glob pattern or a list of paths.

• model_id (str) – Model ID. Must start with rf_, vqsr_, or if_.

• num_partitions (int) – Number of partitions for the output HT.

• import_header_path (Optional[str]) – Optional header file to use for import.

• array_elements_required (bool) – Value passed to hl.import_vcf.

• is_split (bool) – Whether the VCF is already split.

• deduplicate_check (bool) – Whether to remove duplicate variants.

Return type:

Union[Table, Tuple[Table, Table]]

Returns:

HT (or split, unsplit HTs) containing variant QC results.

gnomad_qc.v5.variant_qc.import_variant_qc_vcf.main(args)

Load a single variant QC result VCF into a Hail Table.