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SimWalk2: Mistyping Output Files

The TYPNG-nn.mmm files contain the overall probability of mistyping at each observed genotype, for each original pedigree. These probabilities take into account Mendelian inconsistencies and those mistypings consistent with Mendelian inheritance. In fact, a probability of mistyping is provided for each observed allele.

All genotypes with mistyping probabilities that exceed the significance threshold set in batch item #42 (default value 0.50) are flagged using a double hash mark ( ##). Thus all such genotypes can be quickly seen by searching for ' ##' in the output files (in Unix/Linux/Mac systems this can be accomplished from the command line in a terminal window by issuing the command "grep -h ' ##' TYPNG*").

In these output files the individuals appear in the same order as the pedigree data file and the marker loci in the order specified by the map data file. (Of course, the pedigree, individuals and loci are labeled as well.)

The PEDNU-nn.mmm files echo the original pedigrees, except that each "mistyped genotype" is blanked out. Here "mistyped genotype" is defined as a genotype with mistyping probability above the threshold for significant mistyping set in batch item #42.

The AEKEY-nn.TXT file lists the allele names at each marker. The AEF-nn.ALL file then lists the imputed, expected allele counts at each genotype for each allele named in AEKEY-nn.TXT at that marker. These files can be used by other programs employing the measured genotype approach to study association to quantitative trait loci.

The XOVER-nn.ALL file contains the observed and expected number of crossovers found in this analysis. Also, the resulting p-value for each marker interval recombination fraction is reported.

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