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

added vcf parsing for freebayes and sanity check for gff parsing #17

Merged
merged 7 commits into from
Nov 13, 2024

Conversation

jonas-fuchs
Copy link
Owner

Currently virheat did not support if there were multiple variants associated to one position (e.g. FreeBayes caller). This now allows parsing of these vcf files.

@jonas-fuchs jonas-fuchs added the enhancement New feature or request label Nov 12, 2024
@jonas-fuchs jonas-fuchs linked an issue Nov 12, 2024 that may be closed by this pull request
@hoelzer
Copy link

hoelzer commented Nov 12, 2024

@jonas-fuchs works and looks fine!

It is just a big plot then ;) See here:

virHEAT_plot.pdf

So, we will probably anyway also do some pre-filtering of the VCFs. But then it's nice that we can directly dump the resulting VCFs into your script and it will split off the multi AF fields

@jonas-fuchs jonas-fuchs linked an issue Nov 13, 2024 that may be closed by this pull request
@jonas-fuchs jonas-fuchs changed the title added vcf parsing for freebayes added vcf parsing for freebayes and sanity check for gff parsing Nov 13, 2024
@hoelzer
Copy link

hoelzer commented Nov 13, 2024

Screenshot 2024-11-13 at 09 33 10

nice, the lazy fix works for me! thx!

@jonas-fuchs jonas-fuchs merged commit 1ca41d6 into master Nov 13, 2024
2 checks passed
@jonas-fuchs jonas-fuchs deleted the FreeBayes_parsing branch November 13, 2024 08:43
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement New feature or request
Projects
None yet
Development

Successfully merging this pull request may close these issues.

GFF error when using a mtDNA annotation file Adapting the script for mtDNA
2 participants