Changes

== Useful Wiki Pages ==

== Useful Wiki Pages ==

* To analyse the first study, we execute the following command:  

* To analyse the first study, we execute the following command:  

   raremetalworker  --ped example1.ped --dat example1.dat --vcf example1.vcf.gz --traitName QT1  

   raremetalworker  --ped example1.ped --dat example1.dat --vcf example1.vcf.gz --traitName QT1 \

                   --inverseNormal --makeResiduals --kinSave --kinGeno --prefix STUDY1 --labelHits

                   --inverseNormal --makeResiduals --kinSave --kinGeno --prefix STUDY1  

This command transforms phenotypes to normality (--inverseNormal), calculates trait residuals after adjusting for covariates (--makeResiduals), estimates relatedness between individuals and saves this for later use (--kinSave and --kinGeno), and even generates some annotated PDF files summarizing results (--labelHits).

This command transforms phenotypes to normality (--inverseNormal), calculates trait residuals after adjusting for covariates (--makeResiduals), estimates relatedness between individuals and saves this for later use (--kinSave and --kinGeno), and even generates some PDF files summarizing results.

* After RAREMETALWORKER finishes running, you will see several output files:

* After RAREMETALWORKER finishes running, you will see several output files:

* We next analyse the second study using a similar command:

* We next analyse the second study using a similar command:

   raremetalworker  --ped example2.ped --dat example2.dat --vcf example2.vcf.gz --traitName QT1  

   raremetalworker  --ped example2.ped --dat example2.dat --vcf example2.vcf.gz --traitName QT1 \

                     --inverseNormal --makeResiduals --kinSave --kinGeno --prefix STUDY2 --labelHits

                     --inverseNormal --makeResiduals --kinSave --kinGeno --prefix STUDY2

==STEP 3: Run RAREMETAL for Meta-Analysis==

==STEP 3: Run RAREMETAL for Meta-Analysis==

   tabix -c "#" -s 1 -b 2 -e 2 STUDY2.QT1.singlevar.cov.txt.gz

   tabix -c "#" -s 1 -b 2 -e 2 STUDY2.QT1.singlevar.cov.txt.gz

* We next create two text files that will drive the meta-analysis. The first file lists the input files with summary statistics. Let's call it summaryfiles. In most Linux workstations, you can use the command pico or nano to create this file. These should be the contents of "summaryfiles":

* We next create two text files that will drive the meta-analysis. The first file lists the input files with summary statistics. Let's call it summaryfiles. In most Linux workstations, you can use the command pico or nano to create this file. These should be the contents of "summaryfiles":

   STUDY1.QT1.singlevar.score.txt.gz

   STUDY1.QT1.singlevar.score.txt.gz

* Now, we are ready for meta-analysis. To perform single variant and gene-level meta-analyses all at once, use the following command:

* Now, we are ready for meta-analysis. To perform single variant and gene-level meta-analyses all at once, use the following command:

   raremetal --summaryFiles summaryfiles --covFiles covfiles --groupFile group.file --SKAT --burden --MB --VT  

   raremetal --summaryFiles summaryfiles --covFiles covfiles --groupFile group.file \

            --hwe 1.0e-05 --callRate 0.95 --longOutput --tabulateHits --hitsCutoff 1e-05 --prefix COMBINED.QT1 --labelHits

            --SKAT --burden --MB --VT --longOutput --tabulateHits --hitsCutoff 1e-05 \

            --prefix COMBINED.QT1 --hwe 1.0e-05 --callRate 0.95 -

'''Challenge:''' To ensure the command runs properly, you will have to find "group.file", which tells RAREMETAL which variants to group in gene level tests and copy it to the current directory.  

This command filters summary statistics based on HWE p-value and variant call rate, generates single variant meta-analysis results, generates gene-level meta-analysis results using simple burden test, variable threshold test, Madson-Browning weighted burden test, and SKAT, tabulates significant genes with detailed single variant results included, and even generates some PDF files summarizing results.

* The following output will be generated:

* The following output will be generated:

* For example, RAREMETAL can carry out conditional analyses using the summary statistics in summaryfiles and covfiles.  

* For example, RAREMETAL can carry out conditional analyses using the summary statistics in summaryfiles and covfiles.  

* To carry out a conditional analysis, create a text file that specifies the variant that you want to condition on (lets call it "conditioningfile") and add --condition conditioningfile to the command line. The "conditioningfile" might look like this:

* To carry out a conditional analysis, create a text file that specifies the variant that you want to condition on (lets call it "conditioningfile") and add "--condition conditioningfile" to the command line. The "conditioningfile" might look like this:

   9:505484545:C:T

   9:505484545:C:T