VarScan

--min-coverage    Minimum read depth at a position to make a call [8]
--min-reads2    Minimum supporting reads at a position to call variants [2]
--min-avg-qual    Minimum base quality at a position to count a read [15]
--min-var-freq    Minimum variant allele frequency threshold [0.01]
--min-freq-for-hom    Minimum frequency to call homozygote [0.75]
--p-value    Default p-value threshold for calling variants [99e-02]
--strand-filter    Ignore variants with >90% support on one strand [1]
--output-vcf    If set to 1, outputs in VCF format
--variants    Report only variant (SNP/indel) positions (mpileup2cns only) [0]

Chrom        chromosome name
Position    position (1-based)
Ref            reference allele at this position
Var            variant allele observed
PoolCall    Cross-sample call using all data (Cons:Cov:Reads1:Reads2:Freq:P-value)
Cons - consensus genotype in IUPAC format
Cov - total depth of coverage
Reads1 - number of reads supporting reference
Reads2 - number of reads supporting variant
Freq - the variant allele frequency by read count
P-value - FET p-value of observed reads vs expected non-variant
StrandFilt    Information to look for strand bias using all reads, format R1+:R1-:R2+:R2-:pval
R1+ = reference supporting reads on forward strand
R1- = reference supporting reads on reverse strand
R2+ = variant supporting reads on forward strand
R2- = variant supporting reads on reverse strand
pval = FET p-value for strand distribution, R1 versus R2
SamplesRef    Number of samples called reference (wildtype)
SamplesHet    Number of samples called heterozygous-variant
SamplesHom    Number of samples called homozygous-variant
SamplesNC    Number of samples not covered / not called
SampleCalls    The calls for each sample in the mpileup, space-delimited. Each sample has six values separated by colons:
    Cons - consensus genotype in IUPAC format
    Cov - total depth of coverage
    Reads1 - number of reads supporting reference
    Reads2 - number of reads supporting variant
    Freq - the variant allele frequency by read count
    P-value - FET p-value of observed reads vs expected non-variant