deepgenomics / deepgenomics/GenomeKit
Quickstart VCFTable example doesn't work
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- Python
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Description
Trying to open the file in the example results in this error:
```
>>> vcf = VCFTable.from_vcf("test.vcf.gz", Genome("hg19"), info_ids=["AF"], fmt_ids=["GT", "AD"])
Traceback (most recent call last):
File "", line 1, in
File "/Users/foo/GenomeKit/genome_kit/vcf_table.py", line 247, in from_vcf
VCFTable.build_vcfbin(
ValueError: src/variant_table.cpp:983: In VCF file: test.vcf.gz:9
src/variant_table.cpp:751: Invalid REF "-".
```
The correct contents of the file are in demos/query_vcf.py
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