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Created page with "Category:Software RAREMETAL use summary statistics files to perform meta-analysis. These includes (1) score statistics file and (2) covariance file. Both RAREMETALWORKE..."
[[Category:Software]]

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 generates prefix.traitName.singlevar.score.txt, e.g. prefix.HDL.singlevar.score.txt

##ProgramName=RareMetalWorker
##Version=0.0.7
##Samples=2778
##AnalyzedSamples=2778
##Families=2778
##AnalyzedFamilies=2778
##Founders=2778
##AnalyzedFounders=2778
##Covariates=sex,age,age2,pc1,pc2
##CovariateSummaries min 25th median 75th max mean variance
##sex 1 1 1 2 2 1.33873 0.224074
##age 21 54 65 73 91 63.0734 157.295
##age2 441 2916 4225 5329 8281 4135.5 2.33363e+06
##pc1 -0.1834 -0.0039 0.0016 0.0068 0.026 0.000368719 0.000147096
##pc2 -0.0942 -0.007 -0.001 0.0053 0.0912 -0.000418035 0.000150827
##InverseNormal=ON
##TraitSummaries min 25th median 75th max mean variance
##HDL -3.5797 -0.6737 -0.0052 0.6694 3.5797 0.000389273 0.997184
##AnalyzedTrait -3.56781 -0.67449 -0.000451157 0.673357 3.56781 3.01766e-11 0.999888
##Heritability=0%
#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 564766 T C 2778 0.220122 0.220122 1223 1 0 2166 1 611 -51.7512 43.6541 -0.0271435 0.235827
1 564862 T C 2778 0 0 5556 1 1 0 0 2778 0 0 nan nan
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

* 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 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 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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