Ingest Samples
Indexed files are required for ingestion. If your VCF/BCF files have not been indexed, you can use
bcftoolsto do so:for f in data/vcfs/*.vcf.gz; do bcftools index -c $f; done
You can ingest samples into an already created dataset as follows:
Python
CLI
import tiledbvcf
uri = "my_vcf_dataset"
ds = tiledbvcf.Dataset(uri, mode = "w")
ds.ingest_samples(sample_uris = ["sample_1", "samples_2"])
Just add a regular expression for the VCF file locations at the end of the
store command:tiledbvcf store --uri my_vcf_dataset *.bcf
Alternatively, provide a text file with the absolute locations of the VCF files, separated by a new line:
tiledbvcf store --uri my_vcf_dataset --samples-file samples.txt
Incremental updates work in the same manner as the ingestion above, nothing special is needed. In addition, the ingestion is thread- and process-safe and, therefore, can be performed in parallel.
Last modified 1yr ago