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sigven / vcf2tsvpy

Genomic VCF to tab-separated values
MIT License
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Segmentation fault #8

Closed parnaljoshi closed 1 year ago

parnaljoshi commented 2 years ago

Hi, I am running vcf2tsv on an annotated VCF file, and getting this error:

> python3 vcf2tsv.py myhg38.hg38_multianno.vcf myhg38.hg38_multianno.tab
[W::vcf_parse] INFO '.' is not defined in the header, assuming Type=String
[W::vcf_parse] INFO 'REVEL_rankscor' is not defined in the header, assuming Type=String
Segmentation fault

How can I resolve this? Any help would be greatly appreciated, thanks!

sigven commented 2 years ago

Hey,

Thanks for using the tool :-)

First: I have just updated the tool (and even renamed it to vcf2tsvpy), so I would appreciate if you could install the latest Conda-based version. Here, you use the tool as follows:

vcf2tsvpy --input_vcf <example.vcf.gz> --out_tsv <example.tsv>

The command you indicate above (python3 vcf2tsvpy ..) stems back to an old version of the tool.

Once you have installed the tool succesfully, I would also recommend that you, prior to running vcf2tsvpy, compress and index your input VCF (myhg38.hg38_multianno.vcf) with bgzip + tabix.

It might be that the cause of your error comes from errors in the input VCF, but I recommend you try the above first, and see what that gives you.

cheers, Sigve