Comments (4)
henrydavidge
commented on June 9, 2024
1
@Hoeze we don't have any plans at the moment since we don't know of users who currently have data in tiledb. Definitely something we're paying attention to, though. Also, since Glow operates directly on Spark DataFrames, a generic Spark datasource for tiledb should make it possible to use the Glow functions on data in tiledb.
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Hoeze
commented on June 9, 2024
TileDB-VCF seems to be the successor of GenomicsDB. It has IMHO better support for Spark and it also supports other languages like Python:
https://docs.tiledb.com/main/use-cases/genomics
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nalinigans
commented on June 9, 2024
@Hoeze, GenomicsDB is under continuous development. At the moment, GenomicsDB is being used by multiple gatk tools and I think you should be able to use glow using pipe transformers with gatk.
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henrydavidge
commented on June 9, 2024
I'm going to close this one because if we get to it won't happen for a while.
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Related Issues (20)
- Improve docs: Document usage of schema when reading/writing VCF HOT 2
- VCF files with spaces in the file name cannot be read HOT 4
- configure sparkSession with glow HOT 2
- VEP exone/intron annotations failure HOT 5
- Improve handling of environment variables in the pipe transformer HOT 5
- Installing and running glow outside of databricks HOT 10
- Release with spark3.2 support HOT 1
- Vulnerable shared library might make glow-spark3 vulnerable. Can you help upgrade to patch versions? HOT 5
- Docker build.sh script is not current in tagged release HOT 1
- Ask: add glow to chocolatey HOT 4
- VCF Infinity/NaN values are not handled according to VCF spec
- PySpark 3.3 support HOT 8
- Load glow mave package from Python HOT 5
- spark.read.format("vcf").load() fails for vcf.bgz files HOT 3
- Cannot write INFO fields with LongType to VCF HOT 2
- Python tests fail with KeyError: '_glow_regression_values' HOT 1
- Logistic regression ValueError: Null fit failed! HOT 2
- AnalysisException: Column 'num_workers' does not exist. HOT 1
- pipe transformer support for file input/output for command line apps HOT 2
- Interaction Tests with GLOW HOT 1
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