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[[Category:Software]]
= Overview =
A few rare variants tests (Li-Leal's CMC and Madsen-Browning's weighted method) are implemented in the logisitc regression framework using C++.
The source code is located at wonderland:/home/youna/prj/RV/RV3Tests.v1/
The binary file is located at wonderland:/home/youna/prj/RV/RV3Tests.v1/executables/rvTests
= Example =
See a detailed [[example]] here.
= Syntax =
This software uses command line interface as follows
RARE VARIANT ANALYSIS OPTIONS:
GENOTYPE : --genofile [pos.012],
--geneList [outGeneSorted.txt], --cutoff [0.010],
--collapseChoice [or]
PHENOTYPE : --phenofile [LDL.y.ID]
COVARIATES : --covConsider, --covfile [covFile.ID.2.txt]
PERMUTATION : --nPermute [10], --PermutationSeed [1]
GENE LEVEL TEST RESULT : --geneGlobalTestOut [globalPermuteSummary.txt],
--geneTestpvalueFile [geneTestPvalues.txt]
;GENOTYPE
;--genofile: A genotype 012 matrix (.012 is the file) This file can be prepared by using the prepare012s
source code (wonderland:/home/youna/prj/RV/vcfReader.v1)
binary file (wonderland:/home/youna/prj/RV/vcfReader.v1/executables/prepare012s)
Note: If you going to analyze nonsynonymous and stop annotated variants,
you should use Yanming's vcf annotation [http://genome.sph.umich.edu/wiki/VcfCodingSnps] on the vcf file.
Data File PREPARATION
Input files : --vcf [LDL.test.vcf], --log [], --IDfile []
Subsetting choices : --All
Output files : --outputPrefix [subsetGeno],
--outputGeneList [LDL.geneList.txt]
--vcf: Input vcf file
--log: This is the log file from Yanming's annotation output, we use this log to obtain the gene list
--IDfile specifies a file with one column of subject IDs to subject from the vcf file.
If it is not specified, then all subjects are included for the format conversion.
--All: specifies 1 to include all variants and 0 to include only nonsyn and stop annotated variants.
-- outputPrefix: Specify the prefix for the four output files which will be used in rvTests
*.012: A genotype matrix with subjects as rows and variant sites as columns.
*.012.pos: Chromosome and position numbers.
*.012.indv: Subject IDs.
*.012.frq: The frequency of the included variants.
--outputGeneList: Specify a file to store the gene list which will be used in rvTest.
The list file looks like this
1 OR4F5 69090 70008
1 SAMD11 860529 871276
1 NOC2L 879583 893918
1 KLHL17 895966 901095
1 PLEKHN1 901876 910482
1 C1orf170 910578 912021
;--geneList: This file is an output from prepare012s using the option --outputGeneList with columns as chromosome number, gene Name, start position, end position. There should be no header for this file.
THE CHROMOSOME NUMBERS SHOULD BE NUMERICS!!!! 1 - chromosome 1, DO NOT USE chr1.
;--cutoff: This is the minor allele frequency, you can specify it as 0.01, 0.05 or etc.
;--collapseChoice: Specify one of {or,sum,wt}. or: Li-Leal's CMC test, sum: Use the number of rare variants for each subject as the score, wt: Madeson-Browning's weighted rare variant score.
;PHENOTYPE
;--phenofile: A file where the first column is subject ID and the second column is phenotype (0 or 1).
;COVARIATES
;--covConsider: Default = 0, no covariate is considered. 1. covariate is considered.
;--covfile: Covariate file with the first column as subject ID and the other columns are covariates needed to be considered in the model.
;PERMUTATION
;--nPermute: Number of permutation for the evaluation of p values.
;-- PermutationSeed: Default = 1. Can be changed to other numbers too.
;GENE LEVEL TEST RESULT:
;--geneGlobalTestOut: This file stores the 5% and 95% quantiles of the p values for all the genes at each permutation
;--geneTestPvalueFile: This file gives you the gene name, number of rare variants, count of variants in case/control and p values from the RV test specified by collapseChoice.
