Skip to content
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

decompose_blocksub cannot handle REF properly #96

Open
Fohlen opened this issue Nov 19, 2018 · 0 comments
Open

decompose_blocksub cannot handle REF properly #96

Fohlen opened this issue Nov 19, 2018 · 0 comments

Comments

@Fohlen
Copy link

Fohlen commented Nov 19, 2018

Hello Adrian
Apparently the decompose_blocksub tool does not produce proper VCF's in respect to REF types. You can see this demonstrated here. The filtered.vcf has been produced by processing multiple samples from a control DNA korell with freebayes, breaking them with breakmulti and filtering them. However decompose_blocksub will attempt to break REF fields further, which they should not (a R type should always contain 2 elements).

Further it will throw an exception on MISSING samples, which might or might not be desired behaviour depending on your implementation.

Thanks a lot.
Fohlen

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant