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Old 10-22-2012, 09:13 AM   #3
Location: St. Louis

Join Date: Mar 2009
Posts: 62

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:
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