- gcloud alpha genomics variants import - imports variants into Google Genomics
gcloud alpha genomics variants import --source-uris=SOURCE_URIS,[SOURCE_URIS,...] --variantset-id=VARIANTSET_ID [--file-format=FILE_FORMAT; default="vcf"] [--info-merge-config=INFO_MERGE_CONFIG,[...]] [--normalize-reference-names] [GCLOUD_WIDE_FLAG ...]
(ALPHA) Import variants from VCF or MasterVar files that are in Google
A comma-delimited list of URI patterns referencing existing VCF or MasterVar
files in Google Cloud Storage.
The ID of the destination variant set.
- --file-format=FILE_FORMAT; default="vcf"
Set the file format of the --source-uris. FILE_FORMAT must be one
of: complete-genomics, vcf.
A mapping between VCF INFO field keys and the operations to be performed on
them. Valid operations include: IGNORE_NEW - By default, variant info fields
are persisted if the variant does not yet exist in the variant set. If the
variant is equivalent to a variant already in the variant set, the incoming
variant's info field is ignored in favor of that of the already persisted
variant. MOVE_TO_CALLS - Removes an info field from the incoming variant and
persists this info field in each of the incoming variant's calls.
Convert reference names to the canonical representation. hg19 haplotypes (those
reference names containing "hap") are not modified in any way. All other
reference names are modified according to the following rules: The reference
name is capitalized. The "chr" prefix is dropped for all autosomes and sex
chromsomes. For example "chr17" becomes "17" and "chrX" becomes "X". All
mitochondrial chromosomes ("chrM", "chrMT", etc) become "MT".
GCLOUD WIDE FLAGS
These flags are available to all commands: --account, --configuration, --flags-file, --flatten, --format, --help, --log-http, --project, --quiet, --trace-token, --user-output-enabled, --verbosity. Run $ gcloud help for details.
This command is currently in ALPHA and may change without notice. If this command fails with API permission errors despite specifying the right project, you will have to apply for early access and have your projects registered on the API whitelist to use it. To do so, contact Support at cloud.google.com/support