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| + | [[Category:RAREMETALWORKER]] |
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| '''RAREMETALWORKER''' is a tool for single variant analysis, generating summary statistics for gene level meta analyses in [http://genome.sph.umich.edu/wiki/RAREMETAL '''RAREMETAL''']. | | '''RAREMETALWORKER''' is a tool for single variant analysis, generating summary statistics for gene level meta analyses in [http://genome.sph.umich.edu/wiki/RAREMETAL '''RAREMETAL''']. |
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| If you feel this program is useful, please tell us your name and contact in this [https://docs.google.com/spreadsheet/ccc?key=0AuYjznTeEDYudFpqUk9sQ2pkN3d3endjYldqMEp6ZUE&usp=sharing '''registration''']. | | If you feel this program is useful, please tell us your name and contact in this [https://docs.google.com/spreadsheet/ccc?key=0AuYjznTeEDYudFpqUk9sQ2pkN3d3endjYldqMEp6ZUE&usp=sharing '''registration''']. |
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− | If you have any questions, please contact [[Shuang Feng|'''Shuang Feng''']] sfengsph at umich dot edu or [[Goncalo_Abecasis | '''Goncalo Abecasis''']] goncalo at umich dot edu. | + | If you have any questions, please contact Sai Chen (saichen at umich dot edu) or [[Goncalo_Abecasis | '''Goncalo Abecasis''']] (goncalo at umich dot edu). |
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| * The [[RAREMETAL_Documentation | '''RAREMETAL documentation''']] | | * The [[RAREMETAL_Documentation | '''RAREMETAL documentation''']] |
| * The [[RAREMETAL FAQ | '''FAQ''']] | | * The [[RAREMETAL FAQ | '''FAQ''']] |
| + | * The [[RAREMETAL_Change_Log | '''Change Log''']] |
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| == Key Features == | | == Key Features == |
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| * If --zip option is used, then the following will be generated automatically: | | * If --zip option is used, then the following will be generated automatically: |
| prefix.traitName.singlevar.score.txt.gz | | prefix.traitName.singlevar.score.txt.gz |
| + | prefix.traitName.singlevar.score.txt.gz.tbi |
| prefix.traitName.singlevar.cov.txt.gz | | prefix.traitName.singlevar.cov.txt.gz |
| + | prefix.traitName.singlevar.cov.txt.gz.tbi |
| prefix.singlevar.log | | prefix.singlevar.log |
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| * prefix.traitName.singlevar.cov.txt 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: | | * prefix.traitName.singlevar.cov.txt 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: |
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− | CHR POS VAR_POS_IN_WINDOW LD_MATRIX
| + | 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 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 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,
| + | 1 878744 878744,879381,1560000,1864659,1877659 0.000404537,-0.000235215,-1.4455e-05,-8.69137e-06,-3.1027e-05, |
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| =====Genomic Relationship Matrix (GRM)===== | | =====Genomic Relationship Matrix (GRM)===== |