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| [[Category:Software]] | | [[Category:Software]] |
| + | [[Category:RAREMETAL]] |
| + | [[Category:RAREMETALWORKER]] |
| + | [[Category:rvtests]] |
| = Summary Files Specification for RAREMETAL = | | = Summary Files Specification for RAREMETAL = |
| RAREMETAL use summary statistics files to perform meta-analysis. These includes (1) score statistics file and (2) covariance file. | | RAREMETAL use summary statistics files to perform meta-analysis. These includes (1) score statistics file and (2) covariance file. |
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| RAREMETALWORKER generates prefix.traitName.singlevar.score.txt, e.g. prefix.HDL.singlevar.score.txt | | RAREMETALWORKER generates prefix.traitName.singlevar.score.txt, e.g. prefix.HDL.singlevar.score.txt |
| | | |
− | ##ProgramName=RareMetalWorker
| + | ##ProgramName=RareMetalWorker |
− | ##Version=0.0.7
| + | ##Version=0.3.4 |
− | ##Samples=2778
| + | ##Samples=11619 |
− | ##AnalyzedSamples=2778
| + | ##AnalyzedSamples=5916 |
− | ##Families=2778
| + | ##Families=1257 |
− | ##AnalyzedFamilies=2778
| + | ##AnalyzedFamilies=1117 |
− | ##Founders=2778
| + | ##Founders=3611 |
− | ##AnalyzedFounders=2778
| + | ##AnalyzedFounders=1023 |
− | ##Covariates=sex,age,age2,pc1,pc2
| + | ##Covariates=AGE,AGE2,SEX |
− | ##CovariateSummaries min 25th median 75th max mean variance
| + | ##CovariateSummaries min 25th median 75th max mean variance |
− | ##sex 1 1 1 2 2 1.33873 0.224074
| + | ##AGE 14 29.2 41.9 57 101.3 43.5354 311.366 |
− | ##age 21 54 65 73 91 63.0734 157.295 | + | ##AGE2 196 852.64 1755.61 3249 10261.7 2206.65 2.77293e+06 |
− | ##age2 441 2916 4225 5329 8281 4135.5 2.33363e+06
| + | ##SEX 1 1 2 2 2 1.5764 0.244204 |
− | ##pc1 -0.1834 -0.0039 0.0016 0.0068 0.026 0.000368719 0.000147096
| + | ##InverseNormal=ON |
− | ##pc2 -0.0942 -0.007 -0.001 0.0053 0.0912 -0.000418035 0.000150827
| + | ##TraitSummaries min 25th median 75th max mean variance |
− | ##InverseNormal=ON
| + | ##TRAIT 27.4 101.822 125.036 149.922 330.482 127.381 1264.63 |
− | ##TraitSummaries min 25th median 75th max mean variance
| + | ##AnalyzedTrait -3.7613 -0.674224 0.000211852 0.674756 3.7613 -2.32127e-12 0.999947 |
− | ##HDL -3.5797 -0.6737 -0.0052 0.6694 3.5797 0.000389273 0.997184
| + | ##Heritability=33.953% |
− | ##AnalyzedTrait -3.56781 -0.67449 -0.000451157 0.673357 3.56781 3.01766e-11 0.999888
| + | #CHROM POS REF ALT N_INFORMATIVE FOUNDER_AF ALL_AF INFORMATIVE_ALT_AC CALL_RATE HWE_PVALUE N_REF N_HET N_ALT U_STAT SQRT_V_STAT ALT_EFFSIZE PVALUE SE |
− | ##Heritability=0%
| + | 1 762320 C T 5916 0.00635386 0.00388776 46 1 1 5870 46 0 3.42523 6.57314 0.0792763 0.602301 0.152149 |
− | #CHROM POS REF ALT N_INFORMATIVE FOUNDER_AF ALL_AF INFORMATIVE_ALT_AC CALL_RATE HWE_PVALUE N_REF N_HET N_ALT U_STAT SQRT_V_STAT ALT_EFFSIZE PVALUE
| + | 1 865545 G A 5916 0.000488759 8.45166e-05 1 1 1 5915 1 0 1.32644 1.07745 1.14259 0.21829 0.928141 |
− | 1 564766 T C 2778 0.220122 0.220122 1223 1 0 2166 1 611 -51.7512 43.6541 -0.0271435 0.235827
| + | 1 865584 G A 5916 0 0 0 1 1 5916 0 0 NA NA NA NA NA |
− | 1 564862 T C 2778 0 0 5556 1 1 0 0 2778 0 0 nan nan
| + | 1 865628 G A 5916 0.00782014 0.00566261 67 1 1 5849 67 0 16.4313 7.82519 0.268338 0.0357464 0.127813 |
− | 1 565111 T C 2778 0.0170986 0.0170986 95 1 4.19613e-102 2730 1 47 24.0897 13.6258 0.129688 0.0770708
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| === Rvtests Example === | | === Rvtests Example === |
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| 1 564862 T C 2659 NA NA NA NA NA NA NA NA NA NA NA | | 1 564862 T C 2659 NA NA NA NA NA NA NA NA NA NA NA |
| 1 565111 T C 2659 0.0161715 86 1 4.01334e-96 2616 0 43 0.457052 13.0052 0.00270229 0.971965 | | 1 565111 T C 2659 0.0161715 86 1 4.01334e-96 2616 0 43 0.457052 13.0052 0.00270229 0.971965 |
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| == Input covariance test statistic file == | | == Input covariance test statistic file == |