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| [[Category:Software]] | | [[Category:Software]] |
− | | + | = 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. |
| Both [[RAREMETALWORKER|RAREMETALWORKER]] and [http://genome.sph.umich.edu/wiki/Rvtests '''rvtests'''] can generate these summary statistics files. | | Both [[RAREMETALWORKER|RAREMETALWORKER]] and [http://genome.sph.umich.edu/wiki/Rvtests '''rvtests'''] can generate these summary statistics files. |
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| == Input score test statistics file == | | == Input score test statistics file == |
| | | |
− | * Format
| + | === Format === |
| | | |
| Header lines begins with '#' or 'CHROM'. After header part, we listed the meaning of each column as following: | | Header lines begins with '#' or 'CHROM'. After header part, we listed the meaning of each column as following: |
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| # PVALUE P-value | | # PVALUE P-value |
| | | |
− | * RAREMETALWORKER generates prefix.traitName.singlevar.score.txt, e.g. prefix.HDL.singlevar.score.txt
| + | === RAREMETALWORKER === |
| + | |
| + | RAREMETALWORKER generates prefix.traitName.singlevar.score.txt, e.g. prefix.HDL.singlevar.score.txt |
| | | |
| ##ProgramName=RareMetalWorker | | ##ProgramName=RareMetalWorker |
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| 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 | | 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
| + | === Rvtests === |
| + | Rvtests generates prefix.MetaScore.assoc, e.g. prefix.MetaScore.assoc |
| | | |
| ##Samples=2659 | | ##Samples=2659 |
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| 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: | | 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
| + | === Format === |
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| # CHROM Chromosome | | # CHROM Chromosome |
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| # COV (rvtests only) Covariance matrix between test statistics | | # COV (rvtests only) Covariance matrix between test statistics |
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− | * RAREMETALWORKER generates prefix.traitName.singlevar.cov.txt, e.g. prefix.HDL.singlevar.cov.txt
| + | === RAREMETALWORKER === |
| + | RAREMETALWORKER generates prefix.traitName.singlevar.cov.txt, e.g. prefix.HDL.singlevar.cov.txt |
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| CHR POS VAR_POS_IN_WINDOW LD_MATRIX | | CHR POS VAR_POS_IN_WINDOW LD_MATRIX |
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| 1 878744 878744,879381,1560000,1864659,1877659 0.000404537,-0.000235215,-1.4455e-05,-8.69137e-06,-3.1027e-05, | | 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
| + | === Rvtests === |
| + | 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 | | Later version of rvtests will also generate tabix index file, prefix.MetaCov.assoc.gz |
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| 1 878744 1877659 5 878744,879381,1560000,1864659,1877659 0.000404537,-0.000235215,-1.4455e-05,-8.69137e-06,-3.1027e-05 | | 1 878744 1877659 5 878744,879381,1560000,1864659,1877659 0.000404537,-0.000235215,-1.4455e-05,-8.69137e-06,-3.1027e-05 |
| | | |
− | == Contact ==
| + | = 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]). | | 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]). |