Comments (5)
Addtionally, svdb --merge --vcf ERS177302.lumpy.vcf ERS177302.tiddit.vcf > ERS177302.combine.vcf work well.
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We found when we add the delly result "ERS177302.delly.vcf" the error occurred.
Could SVDB solve the delly result?
from svdb.
We found when we add the delly result "ERS177302.delly.vcf" the error occurred.
Could SVDB solve the delly result?
from svdb.
Hello!
And thanks for the detailed information!
SVDB crashes on line 12, while reading the delly vcf:
File "svdb/readVCF.py", line 12, in svdb.readVCF.readVCFLine
here SVDB tries to access the position of the variant (column 2 in the vcf):
posA = int(variation[1])
Column 2 is not present:
IndexError: list index out of range
Delly VCF files are usually fine, they should have all mandatory columns. Maybe the vcf is broken? Have you checked the last lines of it (using tail for instance). Or could it be that the vcf is compressed? I would double check that the file is not compressed, then I would run it through gatk ValidateVariants or similar.
Good luck!
from svdb.
Thank you for your prompt reply!
We found errors in this vcf. Some of the first and last lines did not start with #. After deletion, it runs perfectly.
thank you!
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Related Issues (20)
- Option to disable "Intersection" in set field HOT 5
- Query is failing with UnicodeDecodeError HOT 1
- Query: Only write variants with frequency lower than a given value HOT 1
- What does the frequency mean? HOT 2
- Add new variants to existing database HOT 1
- Refactoring HOT 5
- No_intra flag HOT 1
- Add information for all callers in `INFO` for overlapping events HOT 1
- Bug: missing headers
- Merging BNDs in different chromosomes HOT 3
- Using SVDB for merging VCF files of different samples? HOT 1
- The install document should be updated. HOT 2
- Enhance the FORMAT column of merge subcommand. HOT 2
- set=Intersection is not fully informative; add FOUND_IN tag? HOT 2
- Syntax error with singularity image HOT 2
- main() takes exactly 2 positional arguments (1 given) HOT 1
- UnicodeDecodeError HOT 3
- Only keep one INFO field HOT 1
- List index out of range HOT 1
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