bcftools soft filters (-s)
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!
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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.
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