Comments (2)
kgururaj
commented on May 20, 2024
Hello Shubham,
Yes, all the common fields are stored in every TileDB cell for each sample.
GenomicsDB was developed primarily for storing variant data from many individual samples (many VCFs, each VCF with 1 sample, say from the output of a variant caller) and then jointly querying/processing the data. It doesn't work well when the variant data from multiple samples is already combined into a single VCF.
We have seen this issue before and gave some thought to it. In the end, I gave up trying to make multi-sample VCF import into GenomicsDB efficient.
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shubhamchandak94
commented on May 20, 2024
Thanks for the clarification!
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Related Issues (20)
- Explore using zstd as an optional alternative to using intel zlib from GenomicsDB
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- Add ID field and handle duplicate names in INFO/FMT/FILTER fields correctly in vcf2genomicsdb_init
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