Filter variants in a file by coverage, supporting reads, variant frequency, or average base quality. It is for use with output from pileup2snp or pileup2indel.
java -jar VarScan.jar filter [variants file] OPTIONS
OPTIONS: --min-coverage Minimum read depth at a position to make a call [10] --min-reads2 Minimum supporting reads at a position to call variants [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, from pileup2indel command --output-file File to contain variants passing filters