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]
--p-value       Default p-value threshold for calling variants [99e-02]

Chrom  chromosome name
Position position (1-based)
Ref  reference allele at this position
Cons  Consensus genotype of sample in IUPAC format.
Reads1  reads supporting reference allele
Reads2  reads supporting variant allele
VarFreq  frequency of variant allele by read count
Strands1 strands on which reference allele was observed
Strands2 strands on which variant allele was observed
Qual1  average base quality of reference-supporting read bases
Qual2  average base quality of variant-supporting read bases
Pvalue  Significance of variant read count vs. expected baseline error
MapQual1 Average map quality of ref reads (only useful if in pileup)
MapQual2 Average map quality of var reads (only useful if in pileup)
Reads1Plus Number of reference-supporting reads on + strand
Reads1Minus Number of reference-supporting reads on - strand
Reads2Plus Number of variant-supporting reads on + strand
Reads2Minus Number of variant-supporting reads on - strand
VarAllele Most frequent non-reference allele observed