Why do my sequences end up in excluded_by_diagnostics.txt?

Help and Getting Started
2

Hi @jonr,

The diagnostics rule produces a log file that should contain more details on why your samples were excluded. This should be logs/diagnostics_BA.txt for your specific build.

If you want to skip the diagnostic step, you can specify this in your build file by adding skip_diagnostics to your filter config:

# remove S dropout sequences and sequences without division label in US
filter:
  exclude_where: "division='USA' purpose_of_sequencing='S dropout'"
  # Removing sequences with lower than 99% coverage
  min_length: 25000 # Default is 28500
  # I don't want Omicron sequences that are before autumn 2021.
  min_date: 2021.75
  # Skip diagnostics rule
  skip_diagnostics: True