Comments (3)
Hoeze
commented on June 9, 2024
My query command for obtaining the single file was bcftools view full_file.vcf.gz --regions X:12513180-12513180
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karenfeng
commented on June 9, 2024
Hi @Hoeze, the VCF reader uses the 0-start, half-open (zero-based) coordinate system (see the docs). To convert to the 1-start, fully-closed system, you can add 1 to the start position.
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Hoeze
commented on June 9, 2024
@karenfeng Thank you so much for the explanation!
I was super confused, because all my VCF-transformer results had the correct 1-start results but joining them with my dataset resulted in nearly empty datasets.
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Related Issues (20)
- 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
- Spark version upgrade 3.4, 3.3 HOT 5
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