gcloud_alpha_genomics_readgroupsets_import (1)
NAME
- gcloud alpha genomics readgroupsets import - imports read group sets into a dataset
SYNOPSIS
-
gcloud alpha genomics readgroupsets import --dataset-id=DATASET_ID --source-uris=[SOURCE_URIS,...] [--partition-strategy=PARTITION_STRATEGY] [--reference-set-id=REFERENCE_SET_ID] [GCLOUD_WIDE_FLAG ...]
DESCRIPTION
(ALPHA) Imports read group sets from a set of BAM files in Google Cloud
REQUIRED FLAGS
-
- --dataset-id=DATASET_ID
-
The ID of the dataset the imported read group sets will belong to.
- --source-uris=[SOURCE_URIS,...]
-
Comma separated list of Google Cloud Storage URIs for BAM files
(samtools.github.io/hts-specs/SAMv1.pdf to be imported.
OPTIONAL FLAGS
-
- --partition-strategy=PARTITION_STRATEGY
-
One of "PER_FILE_PER_SAMPLE" or "MERGE_ALL". The partition strategy describes
how read groups from the provided files are partitioned into read group sets. In
general, use PER_FILE_PER_SAMPLE when importing multiple samples from multiple
files and use MERGE_ALL when importing a single sample from multiple files.
Defaults to PER_FILE_PER_SAMPLE
- --reference-set-id=REFERENCE_SET_ID
-
The reference set ID to associate with the imported read group sets. The
reference headers in the provided BAM files will be validated against this ID.
The reference set ID can be used by consumers of your imported read group sets
for more robust reference genome comparison.
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.
EXAMPLES
Import a single BAM file and associate with the GRCh38 reference set:
-
$ gcloud alpha genomics readgroupsets import --dataset-id 123 \
--reference-set-id "EMud_c37lKPXTQ" \
--source-uris "gs://mybucket/reads.bam"
Import a single sample which is sharded across multiple BAM files:
-
$ gcloud alpha genomics readgroupsets import --dataset-id 123 \
--partition-strategy MERGE_ALL \
--source-uris "gs://mybucket/chr?.bam,gs://mybucket/mt.bam"
NOTES
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