bcftools soft filters (-s)

Question

[blur]

Hi, Is there a list somewhere of all possible soft-filters in bcftools? I saw examples with

bcftools filter -s LowQual

but nothing else... thanks!

Answer 1

[Pierre Lindenbaum]

there is no such list of predefined filters. See the manual: https://samtools.github.io/bcftools/bcftools.html

 -s, --soft-filter STRING|+
    annotate FILTER column with STRING or, with +, a unique filter name generated by the program ("Filter%d").

-s LowQual is a user-defined string and it is associated with an expression:

 -e, --exclude EXPRESSION
    exclude sites for which EXPRESSION is true. For valid expressions see EXPRESSIONS.

any variant failing the expression will be flagged with the FILTER.