Hey guys, thanks for this question and I'm sorry it took me this long to find it and answer! The --indel-filter parameter lets you specify a list of indels (called by VarScan pileup2indel) that will be used for filtering false positive SNPs due to local read mis-alignments due to indels. It will remove SNP calls at or within 1 bp of an indel's position (as reported in mpileup).
I'll see about making this distance a user-defined parameter in the next release.
For future help, please try to post in the VarScan Help forum:
http://sourceforge.net/projects/vars.../forum/1073559