The following BCF tool sub commands (annotate and filter) work fine when given a empty VCF file (i.e. an input file only containing a VCF header). With that being said, there is no need to reset the $bcf_annotate_option an empty string. This only causes issues later on when BCF tools is parsing command line arguments. It interprets an empty string as a file with its input name being an empty string:
As so, BCF tools will work with bcf_annotate_option="-e 'INFO/pArtifact < 0.05' " when the VCF file is empty so there is no need to reset the variable.
The following BCF tool sub commands (annotate and filter) work fine when given a empty VCF file (i.e. an input file only containing a VCF header). With that being said, there is no need to reset the
$bcf_annotate_optionan empty string. This only causes issues later on when BCF tools is parsing command line arguments. It interprets an empty string as a file with its input name being an empty string:As so, BCF tools will work with bcf_annotate_option="-e 'INFO/pArtifact < 0.05' " when the VCF file is empty so there is no need to reset the variable.