Currently, removing variant consequences with multiple combinations of terms requires the user knows in advance what combinations they'll need to remove.
E.g., bcftools filter -e "CSQ_Consequence==\"intron_variant\" | CSQ_Consequence==\"non_coding_transcript_variant\"" will remove entries with either of the terms, but won't match them in combination (intron_variant&non_coding_transcript_variant will remain).
Could we change the way this works so that if a variant matches all of the specified terms, it gets removed? It'd remove the need to know the combinations up front, and make the commands easier to deal with.
One caveat I can think of are cases where the user wants to remove all cases matching one term - e.g., remove all variants with intron_variant, ignoring what else is present.
Currently, removing variant consequences with multiple combinations of terms requires the user knows in advance what combinations they'll need to remove.
E.g.,
bcftools filter -e "CSQ_Consequence==\"intron_variant\" | CSQ_Consequence==\"non_coding_transcript_variant\""will remove entries with either of the terms, but won't match them in combination (intron_variant&non_coding_transcript_variantwill remain).Could we change the way this works so that if a variant matches all of the specified terms, it gets removed? It'd remove the need to know the combinations up front, and make the commands easier to deal with.
One caveat I can think of are cases where the user wants to remove all cases matching one term - e.g., remove all variants with
intron_variant, ignoring what else is present.