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| CalcMatch is a C/C++ software developed by Yun Li that compares two sets of pedigree files. It was initially written to compare imputed genotypes with their true/experimental counterpart but can be used to compare the concordance between any two sets of pedigree files. The input data are in standard Merlin/QTDT format (http://www.sph.umich.edu/csg/abecasis/Merlin/tour/input_files.html). | | CalcMatch is a C/C++ software developed by Yun Li that compares two sets of pedigree files. It was initially written to compare imputed genotypes with their true/experimental counterpart but can be used to compare the concordance between any two sets of pedigree files. The input data are in standard Merlin/QTDT format (http://www.sph.umich.edu/csg/abecasis/Merlin/tour/input_files.html). |
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| + | = Options = |
| == --impped --impdat specify one input pedigree set. <br> == | | == --impped --impdat specify one input pedigree set. <br> == |
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− | --trueped --truedat specify the other input pedigree set. | + | == --trueped --truedat specify the other input pedigree set. == |
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− | --match generates a matrix taking values 0,1,2 indicating # of matched alleles. The dimension of the matrix is # of overlapping individuals times # of overlapping markers of the two input pedigree sets. | + | == --match == |
| + | generates a matrix taking values 0,1,2 indicating # of matched alleles. The dimension of the matrix is # of overlapping individuals times # of overlapping markers of the two input pedigree sets. |
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| --bySNP is turned on by default to generate SNP specific measures. The output .bySNP will contain the following 6 fields for each SNP: | | --bySNP is turned on by default to generate SNP specific measures. The output .bySNP will contain the following 6 fields for each SNP: |