REQUIRED FLAGS

--source-uris=SOURCE_URIS,[SOURCE_URIS,...]

A comma-delimited list of URI patterns referencing existing VCF or MasterVar files in Google Cloud Storage.

--variantset-id=VARIANTSET_ID

The ID of the destination variant set.

OPTIONAL FLAGS

--file-format=FILE_FORMAT; default="vcf"

Set the file format of the --source-uris. FILE_FORMAT must be one of: complete-genomics, vcf.

--info-merge-config=INFO_MERGE_CONFIG,[...]

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.

--normalize-reference-names

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

NOTES