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SimWalk2: Haplotype Analysis Output Files

The HAPLO-nn.mmm files contain the result of the simulated annealing haplotype analysis on each of the original pedigrees.These files are self-documented.

The HEF-nn.ALL and PEDRW-nn.mmm files can be used to export the haplotypes to pedigree drawing programs: Cyrillic (Windows) and Pedigree/Draw (MacOS). For more details on using these files, please see the Usage Notes section. Creation of these files is controlled through batch item #43. Also, the file HMNDL-nn.ALL lists the best haplotypes found for each pedigree, in list-directed, comma-separated, Mendel format.

The QUICK-nn.ALL file contains a quick view of the haplotype analysis for all pedigrees. For each non-founder the source for each of their alleles is listed using only two lines. All recombination events are clearly visible.

The RERUN-nn.* files are created to ease the process of rerunning the haplotype analysis on just those pedigrees for which the program has an indication that it may not have found the optimal overall haplotype. For a complete description of the uses of the RERUN-nn.* files, please see the
Usage Notes section. Note that if no pedigrees are found to be candidates for 'rerunning', then the RERUN-nn.* files are deleted when the program terminates.

The TABLE-nn.ALL file contains a summary table of the results of the haplotype analysis on each pedigree. This file also contains the overall recombination statistics per interval and a list of the parameters used in this run of SimWalk2.

Please note that the
Usage Notes section has more details concerning the use of the haplotype export files and how to rerun the program on just those pedigrees which are indicated to need a longer run. Also, note that even after a haplotype analysis has been 'rerun' as described in the Usage Notes section, all the output files will indicate the best overall haplotypes found in all runs so far performed for each pedigree.

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