"no svlen" error!

[alka...@gmail.com]

Dear Brent,

The speed of annotation is really impressive, despite the provision of many files, with multiple parameters each. 

However, I'd like to ask a question and mention an observation that might help other users who use the configurations in the 'example' folder on github:

- The observation is about the 'gnomad.conf' script, the [[annotation]] section has the names in the format of: "gno_ac_all", while in the [[postannotation]] section, they were referred to in the "ac_gnomad_all" format. I had to change this to make it compatible and functional.

- My question I have is: why do I keep getting error messages while the vcfanno was running complaining about some (seems to be related to structural variants) error, all the lines look like:

variant.go:166: no svlen for variant ##:######

## ####### . A(or any other nucleotide) <CN#> . . AF=#.####;AC=#.#####;AN=#.########;DS=phase3-($$$ some ethnicity)

where # is a number digit and $ is a character digit.

The program didn't stop running, it keeps going on while throwing these error lines. When I checked these the coordinates of these lines, I couldn't find them neither in the original vcf, nor in the annotated one. And I have not provided any Structural variants, or CNV annotations.

Providing the -ends options hasn't solved that either. And removing the gnomAD annotation that I've modified doesn't solve it either.

Thanks again for the great tool, it is saving me so much time and efforts.

Best regards,

Ahmed

[Brent Pedersen]

Hi Ahmed, those lines, if I remember right, are in dbsnp. They are
CNVs but the end position is not listed so the VCF parser (vcfgo)
prints a warning, this is not an error.

Thanks for letting me know about the conf file. I'd certainly welcome
a pull-request to fix that! Or an issue on the github repo.

glad to hear vcfanno is working well for you.
-Brent

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[alka...@gmail.com]

Thanks again Brent, you're right, those lines were from the dbSNP, just warnings though. The DB file was successfully generated at the end.

I appreciate your kind help.

Regards,
Ahmed