-
Notifications
You must be signed in to change notification settings - Fork 38
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Failing to run find-sites #121
Comments
It contains the AF tag, but not for all records. The error happens after many records have been processed. |
Hi @johanneskoester , would you run with the attached debug binary and let me know the error? Do note that there is a |
|
The --min-AN has no influence, but looking at the help, maybe my input VCF does not satisfy the requirements. It has the AF field, but e.g. no samples. It is the "known variation VCF" from ensembl.org (https://ftp.ensembl.org/pub/release-110/variation/vcf/homo_sapiens/, merged together those individual chromosome files) that I have modified with bcftools annotate in order to rename the MAF field into AF ( |
ok. I see the problem, it's a classic :( . I am checking |
Here is a debug build with a fix for that if you'd like to try it. |
I will also run it on chr1 from your link and assure that it works |
I run:
and see:
So I think that change should resolve your issue. I'll make a new release and try to reduce the number of times we see that message. |
This is out in v0.2.18: https://github.com/brentp/somalier/releases/tag/v0.2.18 thanks for reporting and let me know if you have any more issues. |
Thanks a lot!!! Super quick! |
I get the following error
The test file is too large to upload here, but I am happy to send it via gdrive if you need it.
The text was updated successfully, but these errors were encountered: