
The following parameters are available.  Ones with "[]" are in effect:
                Base Call File : results/output.vcf (-bname)
           Posterior Threshold :            0.50 (-p99.999)

Additional Options
           Pedigree File : --ped []
      Map Quality Filter : --minMapQuality, --strict
      Total Depth Filter : --minDepth [1], --maxDepth [10000000]
         Position Filter : --positionFile []
       Chromosome Labels : --xChr [X], --yChr [Y], --mito [MT],
                           --xStart [2699520], --xStop [154931044]
       Filtering Options : --hardFilter, --smartFilter, --softFilter [ON]
           Prior Options : --uniformPrior [ON], --robustPrior
                  Output : --verbose
            Sample Names : --glfAliases [testFiles/glfAlias.txt]
   Prefixes and Suffixes : --glfPrefix [], --glfSuffix []

glfMultiples -- SNP calls based on .glf or .glz files
(c) 2008-2011 Goncalo Abecasis, Sebastian Zoellner, Yun Li

Analysis started on Fri Mar  4 09:50:14 2011

Calling genotypes for files ...
testFiles/NA06984.20.1.1000000.glf
testFiles/NA06985.20.1.1000000.glf
testFiles/NA06986.20.1.1000000.glf
testFiles/NA06989.20.1.1000000.glf
testFiles/NA06994.20.1.1000000.glf
testFiles/NA07000.20.1.1000000.glf
testFiles/NA07037.20.1.1000000.glf

Processing section 20 with 63025520 entries
          Missing bases =         8 (0.000%)
        Reference bases =  63025512 (100.000%)
              A/T bases =    504094 (0.800%, 254363 A, 249731 T)
              G/C bases =    435489 (0.691%, 216194 G, 219295 C)
           Depth Filter =         0 bases (0.000%)
     Map Quality Filter =         1 bases (0.000%)
        Non-Polymorphic =    927542 bases (1.472%)
            Transitions =      1527 bases (0.002%)
          Transversions =       666 bases (0.001%)
    Other Polymorphisms =         0 bases (0.000%)
                No call =  62095777 bases (98.525%)

Analysis completed on Fri Mar  4 09:51:18 2011

