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RAREMETAL Documentation

397 bytes added, 22:23, 7 August 2013
Basic Usage Instructions
'''rareMETAL''' requires the following basic input files: summary statistics and covariance matrices of score statistics generated by '''rareMetalWorker''', a file with list of studies to be included and a group file if gene-level meta-analysis is expected.
=====Summary Statistics=====
Files containing summary statistics and LD matrices generated by '''rareMetalWorker''' should be compressed and tabix indexed using the following commands:
 
bgzip study1.singlevar.score.txt
tabix -s 1 -b 2 -e 2 -c "#" study1.singlevar.score.txt.gz
 
bgzip study1.singlevar.cov.txt
tabix -s 1 -b 2 -e 2 -c "#" study1.singlevar.cov.txt.gz
 
=====List of Studies=====
* --studyName option is crucial for '''rareMETAL''' to work. Ignoring this option would lead to FATAL ERROR and '''rareMETAL''' would stop.
* The file should contain the path and prefix of the studies you want to include.
/net/fantasia/home/sfengsph/prj/raremetal/raremetal/bin/META/TwinsUK/TwinsUK.TG.singlevar.cov.txt.gz.tbi
===== Grouping of Rare Variants=====
====== From a Group File ======
* Grouping methods are only necessary when doing gene-based or group-based burden tests in meta-analysis.
* If none of the grouping method is specified, then only single variant meta-analysis will be performed.
C1orf159 1:1021285:G:T 1:1021302:T:C 1:1021315:A:C 1:1021386:G:A 1:1022534:C:T 1:1025751:C:T 1:1026913:C:T
====== From an Annotated VCF File or Output a VCF File to Annotate ======
If --groupFile option is '''NOT''' specified, '''rareMETAL''' will look for an annotated vcf file as blue print for variants to group. Users are also allowed to generate a vcf file based on the superset of variants from pooled samples, and annotate outside rareMETAL. Then, annotated vcf file can be used as input for rareMETAL for gene-level meta-analysis, or group files can be generated based on the annotated vcf file. Detailed description of these options are available. There are also examples of this usage at the bottom of this page.
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