How to combine delly,lumpy,manta and tiddit result? about svdb HOT 5 CLOSED

Addtionally, svdb --merge --vcf ERS177302.lumpy.vcf ERS177302.tiddit.vcf > ERS177302.combine.vcf work well.

from svdb.

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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