Difference between revisions of "RAREMETALWORKER command reference"
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− | ==to be | + | ==== Output Files ==== |
+ | * --prefix is optional. | ||
+ | * If --prefix is not specified, the output file names will be: | ||
+ | traitname.singlevar.score.txt | ||
+ | traitname.singlevar.cov.txt | ||
+ | * Otherwise, the output file names are: | ||
+ | prefix.traitname.singlevar.score.txt | ||
+ | prefix.traitname.singlevar.cov.txt | ||
+ | * --LDwindow specifies the length of the window that LD Matrix should be generated upon each variant. The default is 1MB. | ||
+ | * --zip gives users the option of writing compressed files (bgzip compressed) automatically for convenient sharing. | ||
+ | * --thin tells RMW to thin points when generating QQ plot and Manhattan plots, so the file size is smaller. | ||
+ | * --labelHits tells RMW to to label the hits using pvalue threshold 0.05/(#of variants tested) with gene name, based on human genome build 19. | ||
+ | |||
+ | ==== VC Options ==== | ||
+ | * When --vcShared and --vcX are specified, RMW knows that you want to fit shared environment and/or chromosome X variance component together with genetic component and non-shared environment. | ||
+ | * When --makeResiduals is specified, RMW understands covariates should be read from PED/DAT file. Covariates are modeled as fixed effects. | ||
+ | |||
+ | ==== Trait Options ==== | ||
+ | * --makeResiduals tells RMW to adjust the covariates and analyze residuals instead of the original phenotypes. If either --kinGeno or --kinPedigree option is used, then a variance component model will be fit based on residuals. If the --inverseNormal option is also used, then the residuals will be quantile normalized before fitting variance component model. | ||
+ | * --traitName is created for situations when you have many traits saved in your PED and DAT file, but you are interested in one or a few of them. It can read a file ending with .txt with each trait of interest in a separate line, or trait names separated with "/". An example to handle one trait or multiple traits is in the following: | ||
+ | --traitName LDL | ||
+ | --traitName LDL/HDL/TG | ||
+ | --traitName traitsOfInterest.txt | ||
+ | * If --traitName is not used, all traits in PED/DAT file will be analyzed. | ||
+ | |||
+ | ==== Model Options ==== | ||
+ | * additive model is used in RMW as default. | ||
+ | * --recessive allows additional association results (pvalue, effect size, and standard error) generated using recessive model. If VCF file is used, then non-reference allele is considered the recessive allele. If PED/DAT files are used for genotype, then minor allele is considered the recessive allele. | ||
+ | * --dominant allows additional association results (pvalue, effect size, and standard error) generated using dominant model. If VCF file is used, then non-reference allele is considered the dominant allele. If PED/DAT files are used for genotype, then minor allele is considered the dominant allele. | ||
+ | * --recessive and --dominant options can be used together. | ||
+ | * Recessive and dominant results are stored in separate files. | ||
+ | |||
+ | ==== Kinship Source ==== | ||
+ | * --kinPedigree allows RMW to generate kinship matrix from pedigree, when pedigree information is available. | ||
+ | * --kinGeno informs RMW to generate kinship matrix from all available variants that pass the criteria, specified in --kinMaf and --kinMiss options. The default will take variants with MAF>0.05 and genotype missing rate <0.05. | ||
+ | * --kinGeno option can NOT be used with --kinPedigree or --kinFile option. Only one of three options or none of them can be used in the same run. | ||
+ | * --kinFile let RMW read in a kinship matrix from a file. The first row of the kinship file has to be the sample IDs included in the kinship file. If a sample of interest is not included in the kinship file, fatal error will occur and the program will be terminated. A sample of interest is a sample that is phenotyped and has all covariates measured when --makeResiduals is specified. | ||
+ | * --kinSave allows you to save the kinship matrix. | ||
+ | |||
+ | ==== Kinship Options ==== | ||
+ | * --kinMiss and --kinMaf should be used with --kinGeno together. | ||
+ | * --kinMiss specifies the maximum genotype missing rate when calculating kinship from genotypes. The default is 0.05. | ||
+ | * --kinMaf specifies the minimum minor allele frequency used when calculating kinship from genotypes. The default is 0.05. | ||
+ | |||
+ | ==== Chromosome X ==== | ||
+ | * --xLabel should have a value of a string which specifies how variants on chromosome X are coded. The default is "X". | ||
+ | * --xStart and --xEnd specifies the start and end of non-pseudo-autosomal regions on chromosome X. These options should be specified when --vcX is used. | ||
+ | * The default for --xStart is 2699520 and default for --xEnd is 154931044, according to NCBI genome build 37. | ||
+ | |||
+ | Please refer to the following for the analysis of X-linked variants [[RAREMETALWORKER_X|'''ANALYZING CHROMOSOME X''']]. | ||
+ | |||
+ | {{PhoneHomeParameters|hdr=====|bullet=1}} |
Revision as of 14:03, 9 April 2014
Output Files
- --prefix is optional.
- If --prefix is not specified, the output file names will be:
traitname.singlevar.score.txt traitname.singlevar.cov.txt
- Otherwise, the output file names are:
prefix.traitname.singlevar.score.txt prefix.traitname.singlevar.cov.txt
- --LDwindow specifies the length of the window that LD Matrix should be generated upon each variant. The default is 1MB.
- --zip gives users the option of writing compressed files (bgzip compressed) automatically for convenient sharing.
- --thin tells RMW to thin points when generating QQ plot and Manhattan plots, so the file size is smaller.
- --labelHits tells RMW to to label the hits using pvalue threshold 0.05/(#of variants tested) with gene name, based on human genome build 19.
VC Options
- When --vcShared and --vcX are specified, RMW knows that you want to fit shared environment and/or chromosome X variance component together with genetic component and non-shared environment.
- When --makeResiduals is specified, RMW understands covariates should be read from PED/DAT file. Covariates are modeled as fixed effects.
Trait Options
- --makeResiduals tells RMW to adjust the covariates and analyze residuals instead of the original phenotypes. If either --kinGeno or --kinPedigree option is used, then a variance component model will be fit based on residuals. If the --inverseNormal option is also used, then the residuals will be quantile normalized before fitting variance component model.
- --traitName is created for situations when you have many traits saved in your PED and DAT file, but you are interested in one or a few of them. It can read a file ending with .txt with each trait of interest in a separate line, or trait names separated with "/". An example to handle one trait or multiple traits is in the following:
--traitName LDL --traitName LDL/HDL/TG --traitName traitsOfInterest.txt
- If --traitName is not used, all traits in PED/DAT file will be analyzed.
Model Options
- additive model is used in RMW as default.
- --recessive allows additional association results (pvalue, effect size, and standard error) generated using recessive model. If VCF file is used, then non-reference allele is considered the recessive allele. If PED/DAT files are used for genotype, then minor allele is considered the recessive allele.
- --dominant allows additional association results (pvalue, effect size, and standard error) generated using dominant model. If VCF file is used, then non-reference allele is considered the dominant allele. If PED/DAT files are used for genotype, then minor allele is considered the dominant allele.
- --recessive and --dominant options can be used together.
- Recessive and dominant results are stored in separate files.
Kinship Source
- --kinPedigree allows RMW to generate kinship matrix from pedigree, when pedigree information is available.
- --kinGeno informs RMW to generate kinship matrix from all available variants that pass the criteria, specified in --kinMaf and --kinMiss options. The default will take variants with MAF>0.05 and genotype missing rate <0.05.
- --kinGeno option can NOT be used with --kinPedigree or --kinFile option. Only one of three options or none of them can be used in the same run.
- --kinFile let RMW read in a kinship matrix from a file. The first row of the kinship file has to be the sample IDs included in the kinship file. If a sample of interest is not included in the kinship file, fatal error will occur and the program will be terminated. A sample of interest is a sample that is phenotyped and has all covariates measured when --makeResiduals is specified.
- --kinSave allows you to save the kinship matrix.
Kinship Options
- --kinMiss and --kinMaf should be used with --kinGeno together.
- --kinMiss specifies the maximum genotype missing rate when calculating kinship from genotypes. The default is 0.05.
- --kinMaf specifies the minimum minor allele frequency used when calculating kinship from genotypes. The default is 0.05.
Chromosome X
- --xLabel should have a value of a string which specifies how variants on chromosome X are coded. The default is "X".
- --xStart and --xEnd specifies the start and end of non-pseudo-autosomal regions on chromosome X. These options should be specified when --vcX is used.
- The default for --xStart is 2699520 and default for --xEnd is 154931044, according to NCBI genome build 37.
Please refer to the following for the analysis of X-linked variants ANALYZING CHROMOSOME X.
PhoneHome Parameters
See PhoneHome for more information on how PhoneHome works and what it does.
--noPhoneHome
disables PhoneHome. PhoneHome is enabled by default based on the thinning parameter.
--phoneHomeThinning
(0-100) adjusts the frequency of PhoneHome.- By default,
--phoneHomeThinning
is set to 50, running 50% of the time. - PhoneHome will only occur if the run's random number modulo 100 is less than the --phoneHomeThinning value.
- N/A if
--noPhoneHome
is set.
- By default,