Export to VCF

You can use the TileDB-VCF CLI to export the TileDB-VCF ingested dataset back into VCF formats for downstream analyses, in a lossless way.

While these exports are lossless in terms of the actual data stored, they may not be identical to the original files. For example, fields within the INFO and FORMAT columns may appear in a slightly different order in the exported files.

Basic export

To recreate all of original (single-sample) VCF files simply run the export command and set the --output-formatto v, for VCF.

tiledbvcf export \
  --uri my_vcf_dataset \
  --output-format v \
  --output-dir exported-vcfs

If bcftools is available on your system you can use it to easily examine any of the exported files:

bcftools view --no-header exported-vcfs/G1.vcf

## 1    13350    .    A    <NON_REF>    .    .    END=36258    GT:DP:GQ:MIN_DP:PL    1/0:50:3:43:44,29,99
## 1    42091    .    A    <NON_REF>    .    .    END=101445    GT:DP:GQ:MIN_DP:PL    0/0:8:91:60:35,62,92
## 2    11625    .    T    <NON_REF>    .    .    END=106375    GT:DP:GQ:MIN_DP:PL    0/0:27:72:76:70,30,83
## 3    14580    .    T    <NON_REF>    .    .    END=86190    GT:DP:GQ:MIN_DP:PL    0/1:50:78:41:67,11,43

Filtering variants

The same mechanics covered in the reading for filtering records by sample and genomic region also apply to exporting VCF files.

tiledbvcf export \
  --uri my_vcf_dataset \
  --output-format v \
  --sample-names G1,G2,G3 \
  --regions 4:53227-196092,9:214865-465259 \
  --output-dir exported-filtered-vcfs