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| = Options = | | = Options = |
− | == --impped --impdat specify one input pedigree set. <br> == | + | == --impped --impdat <br> == |
| + | specify one input pedigree set. |
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− | == --trueped --truedat specify the other input pedigree set. == | + | == --trueped --truedat <br> == |
| + | specify the other input pedigree set. |
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| == --match == | | == --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. | | 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: |
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| (1) SNP : SNP name | | (1) SNP : SNP name |
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| (6) maskedG: total number of genotypes evaluated/masked (<=n of course) (I should change the naming to comparedG or evaluatedG) | | (6) maskedG: total number of genotypes evaluated/masked (<=n of course) (I should change the naming to comparedG or evaluatedG) |
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− | <br> --byGeno can be added on top of --bySNP. It will generates the following fields after the 6 fields above: | + | <br> |
| + | |
| + | == --byGeno == |
| + | can be added on top of --bySNP. It will generates the following fields after the 6 fields above: |
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| (7) hetAerr : allelic discordance rate among heterozygotes | | (7) hetAerr : allelic discordance rate among heterozygotes |
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| <br> | | <br> |
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− | --accuracyByGeno is an option I added most recently to represent the above (7-20) information in a different way. Similar to --byGeno, it is used on top of --bySNP. It can be used together with --byGeno. It will generate the following fields, after (7-20) is --byGeno is turned on or after the 6th field otherwise. | + | == --accuracyByGeno == |
| + | Similar to --byGeno, it is used on top of --bySNP. It may be used together with --byGeno. It will generate the following fields, after (7-20) is --byGeno is turned on or after the 6th field otherwise. |
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| (A) almajor: major allele | | (A) almajor: major allele |
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| (F) accuracy22: allelic concordance rate for homozygotes minor allele | | (F) accuracy22: allelic concordance rate for homozygotes minor allele |
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− | <br> --byPerson generates a separate output file .byPerson and contains the following information for each person: | + | <br> |
| + | == --byPerson == |
| + | generates a separate output file .byPerson and contains the following information for each person: |
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| (1) famid | | (1) famid |
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| (7) maskedG | | (7) maskedG |
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− | <br> This --bySNP option is useful if there is potential sample swap or inter-individual difference, e.g., sequencing depth, number of markers genotyped. | + | <br> This --byPerson option is useful if there is potential sample swap or inter-individual difference, e.g., sequencing depth, number of markers genotyped. |
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| + | <br> |
| + | |
| + | == --maskflag --maskped --maskdat == |
| + | CalcMatch compares all genotypes overlapping the two input sets. However, when --maskflag is turned on AND --maskped and --maskdat are specified (I know ...) it compares only the following subset of the overlapping genotypes: genotypes either not found (i.e., individual or marker not included) or missing (included but with value 0/0, N/N, ./. etc) in --maskped / --maskdat. These options are useful when some individuals were masked for some SNPs while others masked for a different set of SNPs. |
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− | <br> CalcMatch compares all genotypes overlapping the two input sets. However, when --maskflag is turned on AND --maskped and --maskdat are specified (I know ...) it compares only the following subset of the overlapping genotypes: genotypes either not found (i.e., individual or marker not included) or missing (included but with value 0/0, N/N, ./. etc) in --maskped / --maskdat. These options are useful when some individuals were masked for some SNPs while others masked for a different set of SNPs.
| + | = example command lines = |