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.

Sign up for GitHub

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

Jump to bottom

TODO: improve filtering of Vcf files (filter_vcf.sh) #1

Open
filippob opened this issue Jan 3, 2023 · 0 comments
Open

TODO: improve filtering of Vcf files (filter_vcf.sh) #1

filippob opened this issue Jan 3, 2023 · 0 comments
Assignees
@filippob @taniabobbo
Labels
good first issue Good for newcomers

Comments

@filippob
Copy link
Owner

filippob commented Jan 3, 2023

  • consider adding filters for sequencing quality (Phred score): with vcftools, the option --minQ can be used
  • explore filtering for individual genotype coverage (not average coverage across all samples): this may be done in vcftools with the option --minDP (DP FORMAT tag must be specified for all sites)
@filippob filippob added the good first issue Good for newcomers label Jan 3, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@filippob filippob

@taniabobbo taniabobbo

Labels
good first issue Good for newcomers
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@filippob @taniabobbo