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RAREMETALWORKER command reference

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==Useful Links==
Here are some useful links to key pages:
* The [[RAREMETALWORKER | '''RAREMETALWORKER documentation''']]* The [[RAREMETALWORKER_METHOD | '''RAREMETALWORKER method''']]* The [[RAREMETALWORKER_SPECIAL_TOPICS | '''RAREMETALWORKER special topics''']]* The [[Tutorial:_RAREMETAL | '''RAREMETALWORKER quick start tutorial''']]* The [[RAREMETAL_FAQ | '''FAQ''']]
==List of Options ==  Options: Input Files : --ped [], --dat [], --vcf [], --dosage, --flagDosage [DS], --noeof Output Files : --prefix [], --LDwindow [1000000], --zip, --thin, --labelHits VC Options : --vcX, --separateX Trait Options : --makeResiduals, --inverseNormal, --traitName [] Model Options : --recessive, --dominant Kinship Source : --kinPedigree, --kinGeno, --kinFile [], --kinxFile [], --kinSave Kinship Options : --kinMaf [0.05], --kinMiss [0.05] Chromosome X : --xLabel [X], --xStart [2699520], --xEnd [154931044], --maleLabel [1], --femaleLabel [2] others : --cpu [1], --kinOnly, --geneMap [../data/refFlat_hg19.txt], --mergedVCFID PhoneHome : --noPhoneHome, --phoneHomeThinning [100]
==Input Files==
* --dosage must be used with --vcf option.
* Description of dosage format in a VCF file can be found in [[RAREMETALWORKER#DOSAGE | '''dosage''']].
* This option let user customize the name of field in VCF file that labels dosage data.
* The default is "DS".
* If you VCF file does not have the BGZF EOF markers, you should use --noeof option to let RAREMETALWORKER skip checking the BGZF EOF markers at the end of the file.
* By issuing --zip, RAREMETALWORKER compress the [[ RAREMETALWORKER#Summary_Statistics| '''summary statistics''']] and [[RAREMETALWORKER#LD_Matrices | '''LD matrices''']] generated automatically, using gzip. And the output zip files will be indexed using tabix.
=== --thin ===
* The default is 154931044 based on Human Genome build 19.
==PhoneHomeOthers=====--noPhoneHomecpu[1]======*--phoneHomeThinning===cpu takes an integer that specifies the number of cpus to use for estimating kinship matrix from genotypes.
*--kinOnly allows users to estimate kinship matrix without any association analysis of any traits included in the data set.
*To also estimate chromosome X kinship, --vcX option should be added in command line.
* --geneMap takes a string describing the path to find mapping file for manhattan plot annotation.
* The default is human genome build 19, saved in raremetal/data/refFlat_hg19.txt.
* ===--prefix is optional. mergedVCFID===* 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.covThis options allows RAREMETALWORKER to recognize VCF samples IDs in "FAMID_PID" format.txt* --LDwindow specifies the length of the window that LD Matrix should be generated upon each variant. The default value 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 plotsOFF, so the which means VCF sample IDs are consistent with PID field in PED 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 ==PhoneHome==* When --vcShared and --vcX are specified, RMW knows that you want to fit shared environment See [[PhoneHome]] for more information on how PhoneHome works 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 effectswhat it does. ==== 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. noPhoneHome==== 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 allelenoPhoneHome disables PhoneHome. * --dominant allows additional association results (pvalue, effect size, and standard error) generated using dominant model. If VCF file PhoneHome is used, then non-reference allele is considered enabled by default based on 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 togetherthinning parameter.* 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 =phoneHomeThinning===* --kinMiss and --kinMaf should be used with --kinGeno together. * --kinMiss specifies the maximum genotype missing rate when calculating kinship from genotypes. The default is phoneHomeThinning (0.05.* --kinMaf specifies 100) adjusts 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 usedPhoneHome.* The default for --xStart is 2699520 and default for --xEnd is 154931044100, according to NCBI genome build 37. Please refer to the following for running 100% of the analysis of X-linked variants [[RAREMETALWORKER_X|'''ANALYZING CHROMOSOME X''']]time{{PhoneHomeParameters|hdr=====|bullet=1}}

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