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A new program, ioSNP.py, has been added and should be used instead of any previous programs/versions.

Use:

usage: ioSNP.py [-h] [-i INPUT] [-n INFORMAT] [-p PEDIGREE] [-m MARKERS]
            [-c CHROM] [-o OUTPUT] [--output2 OUTPUT2] [-u OUTFORMAT]
            [-v VERBOSE]

Converts between the following SNP-formats:
 Alphaimpute Phase Sequenomlist Sequenommatrix Geno DMU Ldhat Genomelist Genomematrix Beagle APT Plink

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT Input file
  -n INFORMAT, --informat INFORMAT Input file format
  -p PEDIGREE, --pedigree PEDIGREE Pedigree file
  -m MARKERS, --markers MARKERS Marker file
  -c CHROM, --chrom CHROM Chromosome
  -o OUTPUT, --output OUTPUT Output file
  --output2 OUTPUT2     Extra output file
  -u OUTFORMAT, --outformat OUTFORMAT Output file format
  -v VERBOSE, --verbose VERBOSE Prints runtime info