The ADDFILTER command allows filters based on simple comparison operators to be applied to input files. For example, the following commands would filter each input file according to the values in columns labeled FREQ and MARKER.
ADDFILTER FREQ > 0.01 ADDFILTER FREQ < 0.99 ADDFILTER MARKER = rs12345
Newer versions of METAL also allow filters that select a set of markers. For example:
ADDFILTER SNP IN (rs12345,rs98765,rs4567)
To clear the current set of filters, use the REMOVEFILTERS command.