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| + | [[Category:RAREMETALWORKER]] |
| ==Useful Links== | | ==Useful Links== |
| | | |
| Here are some useful links to key pages: | | Here are some useful links to key pages: |
− | * [[RAREMETALWORKER | '''RAREMETALWORKER documentation''']] | + | * The [[RAREMETALWORKER | '''RAREMETALWORKER documentation''']] |
− | * [[RAREMETALWORKER_METHOD | '''RAREMETALWORKER method''']] | + | * The [[RAREMETALWORKER_METHOD | '''RAREMETALWORKER method''']] |
− | * [[RAREMETALWORKER_SPECIAL_TOPICS | '''RAREMETALWORKER special topics''']] | + | * The [[RAREMETALWORKER_SPECIAL_TOPICS | '''RAREMETALWORKER special topics''']] |
− | * [[RAREMETAL_FAQ | '''FAQ''']] | + | * The [[Tutorial:_RAREMETAL | '''RAREMETALWORKER quick start tutorial''']] |
| + | * The [[RAREMETAL_FAQ | '''FAQ''']] |
| | | |
− | ==List of Options ==
| + | Options: |
− | | + | Input Files : --ped [], --dat [], --vcf [], --dosage, --flagDosage [DS], |
− | Options:
| + | --noeof |
− | Input Files : --ped [], --dat [], --vcf [], --dosage, --noeof
| + | Output Files : --prefix [], --LDwindow [1000000], --zip, --thin, |
− | Output Files : --prefix [], --LDwindow [1000000], --zip, --thin,
| + | --labelHits |
− | --labelHits
| + | VC Options : --vcX, --separateX |
− | VC Options : --vcX, --separateX
| + | Trait Options : --makeResiduals, --inverseNormal, --traitName [] |
− | Trait Options : --makeResiduals, --inverseNormal, --traitName []
| + | Model Options : --recessive, --dominant |
− | Model Options : --recessive, --dominant
| + | Kinship Source : --kinPedigree, --kinGeno, --kinFile [], --kinxFile [], |
− | Kinship Source : --kinPedigree, --kinGeno, --kinFile [], --kinxFile [],
| + | --kinSave |
− | --kinSave
| + | Kinship Options : --kinMaf [0.05], --kinMiss [0.05] |
− | Kinship Options : --kinMaf [0.05], --kinMiss [0.05]
| + | Chromosome X : --xLabel [X], --xStart [2699520], --xEnd [154931044], |
− | Chromosome X : --xLabel [X], --xStart [2699520], --xEnd [154931044],
| + | --maleLabel [1], --femaleLabel [2] |
− | --maleLabel [1], --femaleLabel [2]
| + | others : --cpu [1], --kinOnly, |
− | PhoneHome : --noPhoneHome, --phoneHomeThinning [100]
| + | --geneMap [../data/refFlat_hg19.txt], --mergedVCFID |
| + | PhoneHome : --noPhoneHome, --phoneHomeThinning [100] |
| | | |
| ==Input Files== | | ==Input Files== |
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| * --dosage must be used with --vcf option. | | * --dosage must be used with --vcf option. |
| * Description of dosage format in a VCF file can be found in [[RAREMETALWORKER#DOSAGE | '''dosage''']]. | | * Description of dosage format in a VCF file can be found in [[RAREMETALWORKER#DOSAGE | '''dosage''']]. |
| + | |
| + | ===--flagDosage=== |
| + | * This option let user customize the name of field in VCF file that labels dosage data. |
| + | * The default is "DS". |
| + | |
| ===--noeof=== | | ===--noeof=== |
| * 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. | | * 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. |
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| ===--zip=== | | ===--zip=== |
− | * By issuing --zip, RAREMETALWORKER compress the [[ RAREMETALWORKER#Summary_Statistics| '''summary statistics''']] and [[RAREMETALWORKER#LD_Matrices | '''LD matrices''']] generated automatically, using gzip. | + | * 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 === | | === --thin === |
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| ===--kinxFile=== | | ===--kinxFile=== |
− | | + | * --kinxFile must be used with --kinFile and --vcX. |
| + | * --kinxFile takes a string of file name of the previously saved GRM for chromosome X. |
| + | * If --kinxFile is not used, but --kinFile your.autosomal.Empirical.Kinship.gz --vcX are issued in a command line, then RAREMETALWORKER will look for a kinship X file named your.autosomal.Empirical.KinshipX.gz. If this file is still not found, a FATAL ERROR will occur. |
| ===--kinSave=== | | ===--kinSave=== |
| + | * This option must be used with --kinGeno. |
| + | * Issuing --kinSave will request [[RAREMETALWORKER]] to store the estimated GMR in a file named yourprefix.Empirical.Kinship.gz. |
| + | * If --vcX is also issued in the command line, then a separate file named yourprefix.Empirical.KinshipX.gz will be generated where the GRM of chromosome X is saved. |
| *For formats of the saved genomic relationship matrix, please refer to [[RAREMETALWORKER#Genomic_Relationship_Matrix_.28GRM.29 | '''format''']]. | | *For formats of the saved genomic relationship matrix, please refer to [[RAREMETALWORKER#Genomic_Relationship_Matrix_.28GRM.29 | '''format''']]. |
| + | |
| ==Kinship Options== | | ==Kinship Options== |
| ===--kinMaf=== | | ===--kinMaf=== |
− | | + | * --kinMaf takes a value that specifies the MAF cutoff for variants to be used to estimate GRMs. |
| + | * The default is 0.05, which means variants with MAF<0.05 are not used for estimating GRMs. |
| ===--kinMiss=== | | ===--kinMiss=== |
| + | * --kinMiss takes a value that specifies the missing genotype cutoff for variants to be used to estimate GRMs. |
| + | * The default is 0.05, which means variants with genotype call rate <0.95 are not used for estimating GRMs. |
| | | |
| ==Chromosome X== | | ==Chromosome X== |
| ===--xLabel=== | | ===--xLabel=== |
| + | * --xLabel takes a string that used as label for chromosome X in your file. |
| + | * The default is "X". |
| + | |
| ===--xStart=== | | ===--xStart=== |
− | [2699520]
| + | * --xStart takes an integer that described the start position of nonPAR region on chromosome X. |
| + | * The default is 2699520 based on Human Genome build 19. |
| + | |
| ===--xEnd=== | | ===--xEnd=== |
− | [154931044],
| + | * --xStart takes an integer that described the end position of nonPAR region on chromosome X. |
| + | * The default is 154931044 based on Human Genome build 19. |
| | | |
− | ==PhoneHome== | + | ==Others== |
− | ===--noPhoneHome=== | + | ===--cpu[1]=== |
− | ===--phoneHomeThinning===
| + | *--cpu takes an integer that specifies the number of cpus to use for estimating kinship matrix from genotypes. |
| | | |
| + | ===--kinOnly=== |
| + | *--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=== |
| + | * --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: | + | * This options allows RAREMETALWORKER to recognize VCF samples IDs in "FAMID_PID" format. |
− | traitname.singlevar.score.txt
| + | * The default value is OFF, which means VCF sample IDs are consistent with PID field in PED file. |
− | traitname.singlevar.cov.txt
| |
− | * Otherwise, the output file names are:
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− | prefix.traitname.singlevar.score.txt
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− | 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.
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| | | |
− | ==== VC Options ==== | + | ==PhoneHome== |
− | * 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. | + | * See [[PhoneHome]] for more information on how PhoneHome works and what it does. |
− | * When --makeResiduals is specified, RMW understands covariates should be read from PED/DAT file. Covariates are modeled as fixed effects.
| + | ===--noPhoneHome=== |
− | | + | * --noPhoneHome disables PhoneHome. |
− | ==== Trait Options ==== | + | * PhoneHome is enabled by default based on the thinning parameter. |
− | * --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.
| + | ===--phoneHomeThinning=== |
− | * --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:
| + | * --phoneHomeThinning (0-100) adjusts the frequency of PhoneHome. |
− | --traitName LDL
| + | * The default is 100, running 100% of the time. |
− | --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.
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− | | |
− | ==== Kinship Source ====
| |
− | * --kinPedigree allows RMW to generate kinship matrix from pedigree, when pedigree information is available.
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− | * --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.
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− | * --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.
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− | * --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.
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− | * --kinSave allows you to save the kinship matrix.
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− | | |
− | ==== 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.
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− | | |
− | ==== Chromosome X ====
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− | * --xLabel should have a value of a string which specifies how variants on chromosome X are coded. The default is "X".
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− | * --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.
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− | * 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''']].
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− | {{PhoneHomeParameters|hdr=====|bullet=1}}
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