| Class | Analysis and data manipulation command |
| Name | test fimpute |
| 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.
Example:
>> 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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