Filter somatic mutation calls to remove clusters of false positives and SNV calls near indels. Note: this is a basic filter. More advanced filtering strategies consider mapping quality, read mismatches, soft-trimming, and other factors when deciding whether or not to filter a variant.
java -jar VarScan.jar somaticFilter [mutations file] OPTIONS
--min-coverage Minimum read depth [10] --min-reads2 Minimum supporting reads for a variant [2] --min-strands2 Minimum # of strands on which variant observed (1 or 2) [1] --min-avg-qual Minimum average base quality for variant-supporting reads [20] --min-var-freq Minimum variant allele frequency threshold [0.20] --p-value Default p-value threshold for calling variants [1e-01] --indel-file File of indels for filtering nearby SNPs --output-file Optional output file for filtered variants