Changes

From Genome Analysis Wiki
Jump to navigationJump to search

Summary Statistics Files Specification for RAREMETAL and rvtests (view source)

Revision as of 11:39, 29 August 2019

226 bytes added ,  11:39, 29 August 2019
Add rmw category tag
Line 1: Line 1:  
[[Category:Software]]
 
[[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.
 
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.
Line 8: Line 11:  
== 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:
Line 31: Line 34:  
# PVALUE                P-value
 
# PVALUE                P-value
   −
* RAREMETALWORKER generates prefix.traitName.singlevar.score.txt, e.g. prefix.HDL.singlevar.score.txt
+
=== RAREMETALWORKER Example ===
 +
 
 +
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
     −
* rvtests generates prefix.MetaScore.assoc, e.g. prefix.MetaScore.assoc
+
=== Rvtests  Example ===
 +
Rvtests generates prefix.MetaScore.assoc, e.g. prefix.MetaScore.assoc
    
   ##Samples=2659
 
   ##Samples=2659
Line 81: Line 86:  
   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
−
      
== Input covariance test statistic file ==
 
== Input covariance test statistic file ==
Line 87: Line 91:  
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 ===
    
# CHROM                  Chromosome
 
# CHROM                  Chromosome
Line 99: Line 103:  
# COV  (rvtests only)                    Covariance matrix between test statistics
 
# COV  (rvtests only)                    Covariance matrix between test statistics
   −
* RAREMETALWORKER generates prefix.traitName.singlevar.cov.txt, e.g. prefix.HDL.singlevar.cov.txt
+
=== RAREMETALWORKER Example ===
 +
RAREMETALWORKER generates prefix.traitName.singlevar.cov.txt, e.g. prefix.HDL.singlevar.cov.txt
 
    
 
    
 
   CHR    POS        VAR_POS_IN_WINDOW                            LD_MATRIX
 
   CHR    POS        VAR_POS_IN_WINDOW                            LD_MATRIX
Line 106: Line 111:  
   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 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
 
Later version of rvtests will also generate tabix index file, prefix.MetaCov.assoc.gz
   Line 114: Line 120:  
   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]).
Abought
32

edits

Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/9003...15131"

Navigation menu