I don't think it's so simple, have a look at the code, varscan calls a method getReadCounts

```

  HashMap<String, String> readCounts = VarScan.getReadCounts(refBase, readBases, readQualities, minAvgQual, mapQualities);
  (...)

/**
 * Counts the number, quality, and strands of each allele from a pileup
 *
 * @param   refBase     Reference base at this position
 * @param   readBases   String of read bases from pileup
 * @param   readQuals   String of read base qualities from pileup
 * @param   minAvgQual  Integer of minimum required base quality to count a base.
 * @return  results     HashMap<String, String> of results for each allele
 */
static HashMap<String, String> getReadCounts(String refBase, String readBases, String readQuals, int minAvgQual, String mapQuals)
{
    HashMap<String, Integer> readCounts = new HashMap<String, Integer>();
    HashMap<String, Integer> readCountsPlus = new HashMap<String, Integer>();
    HashMap<String, Integer> readCountsMinus = new HashMap<String, Integer>();
    HashMap<String, Integer> qualitySum = new HashMap<String, Integer>();
    HashMap<String, Integer> mapQualitySum = new HashMap<String, Integer>();
    HashMap<String, String> strandsSeen = new HashMap<String, String>();

(...) ````