What it does

Lofreq filter tries to eliminate false-positive calls from a list of variants in VCF format.

To this end, it applies a variety of user-configurable filters to the input variants, which all operate on variant attributes expected to be embedded in the VCF input.

Specifically, certain filters expect:

• the QUAL field of the variant records to be set
• any of the following subfields of a variant's INFO field:
  • DP (required for coverage-based filtering)
  • AF (required for filtering based on variant allele frequency)
  • SB (required for filtering on strand bias)
  • DP4 (required for the compound strand bias filter)

Note:

This tool is optimized for posterior filtering of variants called with Lofreq call, which outputs all variant attributes required by the various configurable filters.

If you are using Lofreq filter to filter VCF variant lists produced with other tools, be prepared for surprises.

In general, if any piece of variant information required for applying a given filter is missing from the input data, the tool will try to disable that filter. Watch out for corresponding warnings in the tool's standard output.

In addition, any p-value based filtering on variant qualities may behave incorrectly since different variant callers might use different QUAL scales.