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[[Category:Software]] [[Category:RAREMETAL]] [[Category:RAREMETALWORKER]] [[Category:rvtests]] = Summary Files Specification for RAREMETAL = RAREMETAL use summary statistics files to perform meta-analysis. These includes (1) score statistics file and (2) covariance file. Both [[RAREMETALWORKER|RAREMETALWORKER]] and [http://genome.sph.umich.edu/wiki/Rvtests '''rvtests'''] can generate these summary statistics files. The aim of this wiki page is to explain file formats. == Input score test statistics file == === Format === Header lines begins with '#' or 'CHROM'. After header part, we listed the meaning of each column as following: # CHROM Chromosome # POS Position # REF Reference Allele # ALT Alternative Allele # N_INFORMATIVE Count of individuals with genotype and phenotype # FOUNDER_AF(RAREMETALWORKER only) Allele frequency among founders # ALL_AF(RAREMETALWORKER only) Allele frequency across entire sample # AF(rvtests only) Allele frequency (for related samples, this is adjusted allele frequency) # INFORMATIVE_ALT_AC Copies of the rare allele among samples with genotype and phenotype # CALL_RATE Fraction of called genotypes # HWE_PVALUE Exact Hardy-Weinberg equilibrium p-value # N_REF Count of reference homozygotes # N_HET Count of heterozygotes # N_ALT Count of alternative allele homozygotes # U_STAT Score statistic numerator # SQRT_V_STAT Score statistic denominator # ALT_EFF_SIZE Estimated effect size # PVALUE P-value === RAREMETALWORKER Example === RAREMETALWORKER generates prefix.traitName.singlevar.score.txt, e.g. prefix.HDL.singlevar.score.txt ##ProgramName=RareMetalWorker ##Version=0.3.4 ##Samples=11619 ##AnalyzedSamples=5916 ##Families=1257 ##AnalyzedFamilies=1117 ##Founders=3611 ##AnalyzedFounders=1023 ##Covariates=AGE,AGE2,SEX ##CovariateSummaries min 25th median 75th max mean variance ##AGE 14 29.2 41.9 57 101.3 43.5354 311.366 ##AGE2 196 852.64 1755.61 3249 10261.7 2206.65 2.77293e+06 ##SEX 1 1 2 2 2 1.5764 0.244204 ##InverseNormal=ON ##TraitSummaries min 25th median 75th max mean variance ##TRAIT 27.4 101.822 125.036 149.922 330.482 127.381 1264.63 ##AnalyzedTrait -3.7613 -0.674224 0.000211852 0.674756 3.7613 -2.32127e-12 0.999947 ##Heritability=33.953% #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 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 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 865584 G A 5916 0 0 0 1 1 5916 0 0 NA NA NA NA NA 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 === Rvtests Example === Rvtests generates prefix.MetaScore.assoc, e.g. prefix.MetaScore.assoc ##Samples=2659 ##AnalyzedSamples=2659 ##Families=2659 ##AnalyzedFamilies=2659 ##Founders=2659 ##AnalyzedFounders=2659 ##InverseNormal=ON ##TraitSummary min 25th median 75th max mean variance ##Trait -3.56023 -0.679098 -0.00304512 0.682994 3.56845 0.000710616 1.00065 ##AnalyzedTrait -3.55632 -0.674786 0 0.674786 3.55632 -1.10229e-17 0.999884 ##Covariates=sex,age,age2,pc1,pc2 ##CovariateSummary min 25th median 75th max mean variance ##sex 1 1 1 2 2 1.34524 0.226135 ##age 21 55 66 73 91 63.6491 150.565 ##age2 441 3025 4356 5329 8281 4201.72 2.25458e+06 ##pc1 -0.1946 -0.0041 0.0014 0.0064 0.0246 -0.00027815 0.000184625 ##pc2 -0.0957 -0.0067 -0.0005 0.0062 0.0989 0.000239526 0.000188235 CHROM POS REF ALT N_INFORMATIVE AF INFORMATIVE_ALT_AC CALL_RATE HWE_PVALUE N_REF N_HET N_ALT U_STAT SQRT_V_STAT ALT_EFFSIZE PVALUE 1 564766 T C 2659 0.23223 1235 1 0 2041 1 617 20.546 43.5254 0.0108453 0.636894 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 == Input covariance test statistic file == Covariance test statistics contains the LD matrix among a variant and the adjacent markers within a prefixed-sized window. The default window size is 1MB. It has the following format: === Format === # CHROM Chromosome # CURRENT_POS (RAREMETALWORKER only) Position for the first marker in Window # VAR_POS_IN_WIND (RAREMETALWORKER only) Position for the other markers in window, separated by commas # COV_MATRICES (RAREMETALWORKER only) Covariance matrix between test statistics # START_POS (rvtests only) Position for the first marker in sliding window # END_POS (rvtests only) Position for the last marker in sliding window # NUM_MARKER (rvtests only) Number of markers in the sliding windows # MARKER_POS (rvtests only) Number of marker positions in the sliding windows # COV (rvtests only) Covariance matrix between test statistics === RAREMETALWORKER Example === RAREMETALWORKER generates prefix.traitName.singlevar.cov.txt, e.g. prefix.HDL.singlevar.cov.txt CHR POS VAR_POS_IN_WINDOW LD_MATRIX 1 762320 762320,865628,865665,878744,879381,1560000 0.0359084,-0.000242112,-0.00125797,-0.000993422,-0.000344509,-0.00017077, 1 865628 865628,865665,878744,879381,1560000,1864659 0.419804,-0.0103663,-0.00635265,0.0594056,0.0534505,-0.00462183, 1 878744 878744,879381,1560000,1864659,1877659 0.000404537,-0.000235215,-1.4455e-05,-8.69137e-06,-3.1027e-05, === Rvtests Example === Rvtests generates prefix.MetaCov.assoc.gz, e.g. prefix.HDL.MetaCov.assoc.gz Later version of rvtests will also generate tabix index file, prefix.MetaCov.assoc.gz CHR START_POS END_POS NUM_MARKER MARKER_POS COV 1 762320 1560000 6 762320,865628,865665,878744,879381,1560000 0.0359084,-0.000242112,-0.00125797,-0.000993422,-0.000344509,-0.00017077 1 865628 1864659 6 865628,865665,878744,879381,1560000,1864659 0.419804,-0.0103663,-0.00635265,0.0594056,0.0534505,-0.00462183 1 878744 1877659 5 878744,879381,1560000,1864659,1877659 0.000404537,-0.000235215,-1.4455e-05,-8.69137e-06,-3.1027e-05 = Contact = Please contact Dajiang Liu ([mailto:dajiang@umich.edu]), Xiaowei Zhan ([mailto:zhanxw@umich.edu]), Shuang Feng([mailto:sfengsph@umich.edu]) or Goncalo Abecasis ([mailto:goncalo@umich.edu]).

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