Changes

== Useful Wiki Pages ==

== Useful Wiki Pages ==

* 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

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

   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

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

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

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.

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.