|Class||Analysis and data manipulation command|
|Arguments||<map_file> <genotype_file> [ped_id].|
Compare genotypes for the matching IDs and loci in current dataset to those in the specified FImpute genotype file.
>> read bin current.bin.gz >> file head out/genotypes_imp.txt ID Chip Calls... 0000001 2 30044420032333300330033330030332000220000000 0000002 2 20044420000003300330033330030332333220033300 0000003 2 30033330022220000220022220020222400220000000 >> test fim out/snp_info.txt out/genotypes_imp.txt Comparing current genotypes to FImpute data: NOTE: Merging individual records based in id only. FImpute SNP map file = zzz_output/snp_info.txt Number of arrays/sources = 2 Total number of markers = 62 Number matched = 62 FImpute genotype file = zzz_output/genotypes_imp.txt Read in 22072 individuals 1554464 nonmissing SNP genotypes (0.19 s) Number of concordant genotypes = 1004931 (64.6%) Number of discordant genotypes = 0 (0%) Number of updateable genotypes = 549533 (35.4%)
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