CLI
Available Commands
create
a new datasetstore
specified VCF files in a datasetexport
data from a datasetlist
all sample names present in a datasetstat
prints high-level statistics about a datasetutils
utility functions for dataset
Create
Create an empty TileDB-VCF dataset.
Usage
Options
Flag | Description |
| TileDB dataset URI. |
| Info or format field names (comma-delimited) to store as separate attributes. Names should be |
| Tile capacity to use for the array schema [default |
| Anchor gap size to use [default |
| CSV string of the format |
| Checksum to use for dataset validation on read and writes [default |
| Do not allow records with duplicate end positions to be written to the array. |
Store
Ingests registered samples into a TileDB-VCF dataset.
Usage
Options
Flag | Description |
| TileDB dataset URI. |
| Number of threads [default |
| [S3 only] Part size to use for writes (MB) [default |
| Directory used for local storage of downloaded remote samples. |
| Amount of local storage (in MB) allocated for downloading remote VCF files prior to ingestion [default |
| Max number of BCF records to buffer per file [default |
| Max length (# columns) of an ingestion task. Affects load balancing of ingestion work across threads, and total memory consumption [default |
| The total memory budget (MB) used when submitting TileDB queries [default |
| Enable verbose output. |
| CSV string of the format |
| File with 1 VCF path to be ingested per line. The format can also include an explicit index path on each line, in the format |
| If specified, the samples file ( |
| Number of samples per batch for ingestion [default |
| Enable TileDB stats |
| Enable TileDB stats for vcf header array usage. |
| Resume incomplete ingestion of sample batch. |
Export
Exports data from a TileDB-VCF dataset.
Usage
Options
Flag | Description |
| TileDB dataset URI. |
| Export format. Options are: |
| [TSV export only] The name of the output TSV file. |
| [TSV export only] An ordered CSV list of fields to export in the TSV. A field name can be one of |
| CSV list of regions to export in the format |
| File containing regions (BED format). |
| Do not sort regions or regions file if they are pre-sorted. |
| Only export the first N intersecting records. |
| Directory used for local output of exported samples. |
| Partitions the list of samples to be exported and causes this export to export only a specific partition of them. Specify in the format |
| Partitions the list of regions to be exported and causes this export to export only a specific partition of them. Specify in the format |
| If set, all output file(s) from the export process will be copied to the given directory (or S3 prefix) upon completion. |
| CSV string of the format |
| Enable verbose output. |
| Don't write output files, only print the count of the resulting number of intersecting records. |
| The memory budget (MB) used when submitting TileDB queries [default |
| The percentage of the memory budget to use for TileDB query buffers [default |
| The percentage of the memory budget to use for TileDB tile cache [default |
| File with 1 VCF path to be registered per line. The format can also include an explicit index path on each line, in the format in the format |
| Enable TileDB stats |
| Enable TileDB stats for vcf header array usage. |
| Disable validating that samples passed exist in dataset before executing query and error if any sample requested is not in the dataset. |
| Disable progress estimation in verbose mode. Progress estimation can sometimes cause a performance impact. |
List
Lists all sample names present in a TileDB-VCF dataset.
Usage
Options
Flag | Description |
| TileDB dataset URI. |
| CSV string of the format |
Stat
Prints high-level statistics about a TileDB-VCF dataset.
Usage
Options
Flag | Description |
| TileDB dataset URI. |
| CSV string of the format |
Utils
Utils for working with a TileDB-VCF dataset, such for consolidating and vacuuming fragments or fragment metadata.
Usage
Options
Flag | Description |
| TileDB dataset URI. |
| CSV string of the format |
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