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readme.pregsf90 [2020/05/22 16:41]
dani [Quality Control (QC) for G]
readme.pregsf90 [2023/09/11 18:50] (current)
dani [GWAS options (PostGSF90)]
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     * Field 2 - genotype with 0,1,2 and 5 (missing) or real values for gene content 0.12 ...      * Field 2 - genotype with 0,1,2 and 5 (missing) or real values for gene content 0.12 ... 
  
-Fields need to be separated by at least one space and Field 2 should be fixed format i.e. all rows of genotypes ​should ​start at the same column number!!!+Fields need to be separated by at least one space and Field 2 should be fixed format i.e. all rows of genotypes ​*must* ​start at the same column number!!!
  
 <​file>​ <​file>​
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 </​file>​ </​file>​
  
-An utility program ([[readme.illumina2pregs|illumina2pregs]]) is available to converts Illumina FinalReport and SNP_Map.txt ​in such format. ​+using fractional genotypes is also possible, i.e. from imputation. In this case the genotypes must be "​stick"​ together with **two** decimal places i.e. 
 + 
 +<​file>​ 
 + ​80 ​  ​2.001.001.000.001.00 
 + 8014 2.001.001.001.000.00 
 + ​516 ​ 2.001.001.000.000.00  
 +1032  0.501.120.251.502.00 
 +</​file>​ 
 + 
 +where the last individual has "​fractional"​ genotype ''​0.50 1.12 0.25 1.50 2.00''​. 
 + 
 + 
 +An utility program ([[readme.illumina2pregs|illumina2pregs]]) is available to converts Illumina FinalReport and SNP_Map.txt ​into such format. ​ 
 + 
 +Some useful options: 
 +  * ''​OPTION missingAIPL''​ will read and convert genotype codes ''​3''​ and ''​4''​ as missing, i.e. internally they are read and converted to ''​5''​. 
 +  * ''​OPTION QMSim''​ will read and convert genotype codes ''​3''​ and ''​4''​ as ''​1'',​ i.e. heterozygote. This is useful e.g. if [[https://​animalbiosciences.uoguelph.ca/​~msargol/​qmsim/​|QMSim]] is used to produce the simulations.\ 
 +  * ''​OPTION fastread''​ will use C's library zlib for faster reading (useful for *very* large number of genotypes). This library is always available in all systems and in that case it defaults to standard reading. 
  
 * Renumbered ID for genotypes * Renumbered ID for genotypes
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 Useful for check for Mendelian conflicts and HWE (with also ''​OPTION sex_chr''​) and for GWAS (see ''​PostGSF90''​ program) Useful for check for Mendelian conflicts and HWE (with also ''​OPTION sex_chr''​) and for GWAS (see ''​PostGSF90''​ program)
  
-The //file// should ​has a header with the following column names:\\+The //file// should ​have a header with the following column names:\\
 //SNP_ID// - identification of the SNP (alphanumeric) \\ //SNP_ID// - identification of the SNP (alphanumeric) \\
 //CHR// - chromosome number (numeric), starting from 1 \\ //CHR// - chromosome number (numeric), starting from 1 \\
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-First SNP in the Map fiel corresponds to first SNP in genotype file, and so on.+The first SNP in the Map file corresponds to the first SNP in the genotype file, and so on.
  
-Other alphanumeric ​field are optionals.+Other alphanumeric ​fields ​are optional.
  
 If ''​OPTION saveCleanSNPs''​ is present fields are output. If ''​OPTION saveCleanSNPs''​ is present fields are output.
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 <​file>​ OPTION whichfreq x</​file> ​ <​file>​ OPTION whichfreq x</​file> ​
-   ​specifies what frequencies are used to create **G** in **G=ZDZ**'​. The same frequencies are used to center+   ​specifies what frequencies are used to create **G** in **G=ZDZ**'​/k. The same frequencies are used to center
  Z and to scale in D. The variable //x// can be:  Z and to scale in D. The variable //x// can be:
              *0: read from file ''​freqdata''​ or from other file as specified using ''​OPTION FreqFile''​              *0: read from file ''​freqdata''​ or from other file as specified using ''​OPTION FreqFile''​
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 <​file>​OPTION whichfreqScale x</​file>​ <​file>​OPTION whichfreqScale x</​file>​
-Specifies what frequencies are used to __scale__ **G** in **G=ZDZ**'​. ​+Specifies what frequencies are used to __scale__ **G** in **G=ZDZ**'​/k
 Use this option if, for instance, want to use 0.5 for centering (using option above) but observed 2pq for scaling. ​ Use this option if, for instance, want to use 0.5 for centering (using option above) but observed 2pq for scaling. ​
 The variable //x// can be: The variable //x// can be:
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 Weighting Z*= Z sqrt(D) => G = Z*Z*' = ZDZ'​.\\ Weighting Z*= Z sqrt(D) => G = Z*Z*' = ZDZ'​.\\
 format: one column of weights in the same order as in the genotyped file.\\ format: one column of weights in the same order as in the genotyped file.\\
-Weights can be extracted from output of ''​PostGSF90'' ​program.+Weights can be extracted from the output of ''​PostGSF90''​.
  
 <​file>​OPTION maxsnp x</​file>​ <​file>​OPTION maxsnp x</​file>​
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 <​file>​OPTION outparent_progeny</​file>​ <​file>​OPTION outparent_progeny</​file>​
 Create a full log file (''​Gen_conflicts_all''​) with all pairs of parent-progeny tested for Mendelian conflicts. Create a full log file (''​Gen_conflicts_all''​) with all pairs of parent-progeny tested for Mendelian conflicts.
 +
 +<​file>​OPTION out_snp_exclusion_error_rate</​file>​
 +Create a log file (''​SNP_Mendelian_error_rate''​) with statistics for SNP Mendelian error rate.
  
 <​file>​OPTION excludeCHR n1 n2 n3 ...</​file> ​ <​file>​OPTION excludeCHR n1 n2 n3 ...</​file> ​
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 <​file>​OPTION sex_chr n</​file>​ <​file>​OPTION sex_chr n</​file>​
-Chromosomes number ​equal or greater ​than //n// are not consider ​autosomes.\\+Chromosomes ​with a number greater ​or equal to //n// are not considered as autosomes.\\
 If selected this option, sex chromosomes will not be used for checking parent-progeny Mendelian conflicts, ​ HWE and heritability of gene content\\ If selected this option, sex chromosomes will not be used for checking parent-progeny Mendelian conflicts, ​ HWE and heritability of gene content\\
 but they will be included for all remaining processes. **If you want to remove sex chromosomes**,​ which we do recommend, use ''​OPTION excludeCHR''​. but they will be included for all remaining processes. **If you want to remove sex chromosomes**,​ which we do recommend, use ''​OPTION excludeCHR''​.
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 <​file>​OPTION high_threshold_diagonal_g x</​file>​ <​file>​OPTION high_threshold_diagonal_g x</​file>​
-Check and remove ​individuals with extreme high diagonals in the genomic relationship matrix.\\+Check and provide a list of individuals with extreme high diagonals in the genomic relationship matrix.\\
 If optional //x// is present set the threshold\\ If optional //x// is present set the threshold\\
 default value 1.6 default value 1.6
  
 <​file>​OPTION low_threshold_diagonal_g x</​file>​ <​file>​OPTION low_threshold_diagonal_g x</​file>​
-Check and remove ​individuals with extreme low diagonals in the genomic relationship matrix.\\+Check and provide a list of individuals with extreme low diagonals in the genomic relationship matrix.\\
 If optional //x// is present set the threshold\\ If optional //x// is present set the threshold\\
 default value 0.7 default value 0.7
  
-<​file>​OPTION plotpca</​file>​+<​file>​OPTION plotpca ​<​print/​noprint>​</​file>​
 Plot the first two principal components to look for stratification in the population. ​ Plot the first two principal components to look for stratification in the population. ​
 +
  
 <​file>​OPTION extra_info_pca file col</​file>​ <​file>​OPTION extra_info_pca file col</​file>​
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 <​file>​OPTION LD_by_pos x</​file>​ <​file>​OPTION LD_by_pos x</​file>​
-Calculate LD within chromosome and windows of SNP based on position +Calculate LD within chromosome and windows of SNP based on position. Optional ​parameter x define with windows size in Bp, default value 200000
-optional ​parameter x define with windows size in Bp, default value 200000+
  
 <​file>​OPTION filter_by_LD x</​file>​ <​file>​OPTION filter_by_LD x</​file>​
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 <​file>​OPTION thrWarnCorAG x</​file>​ <​file>​OPTION thrWarnCorAG x</​file>​
 Set the threshold to issue a warning if cor(A22,G) < //x//\\ Set the threshold to issue a warning if cor(A22,G) < //x//\\
-default value 0.5+default value 0.5
  
 <​file>​OPTION thrStopCorAG x</​file>​ <​file>​OPTION thrStopCorAG x</​file>​
 Set the threshold to Stop the analysis if cor(A22,G) < //x//\\ Set the threshold to Stop the analysis if cor(A22,G) < //x//\\
-default ​values ​0.3+default ​value = 0.3
  
 <​file>​OPTION ​ thrCorAG x</​file>​ <​file>​OPTION ​ thrCorAG x</​file>​
 Set the threshold to calculate corr(A22,G) for only A22 >= //​x//​\\ ​ Set the threshold to calculate corr(A22,G) for only A22 >= //​x//​\\ ​
-default ​values ​0.02      ​+default ​value = 0.02      ​
    ​    ​
  
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 and to control bias.\\ and to control bias.\\
  
-The defaults ​values are:+The default ​values are:
  
 tau=1  alpha =0.95  beta = 0.05  gamma=0 ​ delta=0 ​ omega=1 tau=1  alpha =0.95  beta = 0.05  gamma=0 ​ delta=0 ​ omega=1
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 The variable ''​x''​ can be: The variable ''​x''​ can be:
   * 0: no scaling   * 0: no scaling
-  * 1: mean(diag(G))=1,​ mean(offdiag(G))=0 +  * 1: mean(diag(G))=1,​ mean(offdiag(G))=0. This implies that the estimated variance components and mean refer to the genotyped population ​ [[http://​dx.doi.org/​10.1016/​j.tpb.2015.08.005| Legarra, 2016]] 
-  * 2: mean(diag(G))=mean(diag(A22)),​ mean(offdiag(G))=mean(offdiag(A22))  ​(default) +  * 2: mean(diag(G))=mean(diag(A22)),​ mean(offdiag(G))=mean(offdiag(A22))  ​[[http://​journals.cambridge.org/​abstract_S1751731112000742|Christensen et al., 2012]] **This is the default** 
-  * 3: mean(G)=mean(A22) +  * 3: mean(G)=mean(A22) ​[[ https://​www.cambridge.org/​core/​journals/​genetics-research/​article/​bias-in-genomic-predictions-for-populations-under-selection/​7A0ECD4D63EAFD33B1586FA1DE9DCF44|Vitezica et al. (2011)]] 
-  * 4: rescale G using Fst adjustment. As in Powell et al. (2010) ​or Vitezica et al. (2011) ​+  * 4: rescale G using Fst adjustment. As in [[https://​www.nature.com/​articles/​nrg2865|Powell et al. (2010)]] and [[https://​www.cambridge.org/​core/​journals/​genetics-research/​article/​bias-in-genomic-predictions-for-populations-under-selection/​7A0ECD4D63EAFD33B1586FA1DE9DCF44|Vitezica et al. (2011)]]
   * 9: arbitrary parameters: specify two additional numbers $a$ and $b$ in $a+b\mathbf{G}$ as ''​OPTION tunedG 9 a b''​.   * 9: arbitrary parameters: specify two additional numbers $a$ and $b$ in $a+b\mathbf{G}$ as ''​OPTION tunedG 9 a b''​.
 +
 +=====Options to extract the diagonal of H (aka genomic improved inbreeding)=====
 +
 +The diagonal of **H** contains an improved estimator of inbreeding: $\mathbf{F}_H = diag(\mathbf{H})-1$ . For genotyped animals, the diagonal of **H** is identical to the diagonal of **G** , and thus $\mathbf{F}_H=\mathbf{F}_G$ , sometimes called Genomic Inbreeding. The elements of $\mathbf{F}_H$ for non-genotyped animals include pedigree-based estimates of Genomic Inbreeding. See 
 +[[https://​doi.org/​10.1186/​s12711-017-0363-9|Colleau et al 2017]] and [[https://​doi.org/​10.3168/​jds.2019-17750|Legarra et al. 2019]]. The last contains a description of the underlying methods.
 +
 +To extract the diagonal of **H** one of these two ''​OPTION''​s needs to be used:
 +
 +  * ''​OPTION saveDiagH''​ outputs $diag(\mathbf{H})$ with renumbered id's
 +  * ''​OPTION saveDiagHOrig''​ outputs $diag(\mathbf{H})$ with original //and// renumbered id's
 +
 +
 +User can use one of two equivalent methods : 
 +  * 1: using ''​OPTION methodDiagH 1'',​ does a sparse inversion of $\mathbf{H}^{-1}$ (default) . This option is very fast for small to medium pedigrees.
 +  * 2: using ''​OPTION methodDiagH 2'',​ this is in fact Method 3 in [[https://​doi.org/​10.3168/​jds.2019-17750|Legarra et al. 2019]], an outer product ​ method ​ that uses $\mathbf{M}=\mathbf{A}_{22}^{-1}(\mathbf{G}-\mathbf{A}_{22})\mathbf{A}_{22}^{-1}$. This method is **recommended** for large pedigrees as it is (for large pedigrees) less time and memory consuming.
 +
 +The output depends on the method used. ''​OPTION methodDiagH 1''​ shows only individual id and $diag(\mathbf{H})$. ​ ''​OPTION methodDiagH 2''​ shows individual id and the values of $diag(\mathbf{H})$,​ $diag(\mathbf{A})$ (pedigree-based relationship) and the difference $c$ such that $diag(\mathbf{H})=diag(\mathbf{A})+c$. ​
 +
 +An example of the output obtained with ''​OPTION methodDiagH 2''​ and ''​OPTION saveDiagHOrig''​ has original_id,​ $diag(\mathbf{H})$,​ $diag(\mathbf{A})$,​ and the difference $c=diag(\mathbf{H})-diag(\mathbf{A})$,​ and the renumbered_id:​
 +
 +<​code>​
 +testDiagH2_mf andres$ head diagHdirect.txt.2
 +45036060023 ​               1.179829759235491 ​ 1.250322947770358 -0.070493188534867 ​         1
 +64000169880047 ​            ​1.126222691080622 ​ 1.220500000000000 -0.094277308919378 ​         2
 +64000246030053 ​            ​1.168573237141459 ​ 1.237528320312500 -0.068955083171041 ​         3
 +45038980011 ​               1.189937645185136 ​ 1.251295679897070 -0.061358034711934 ​         4
 +</​code>​
 +
  
 =====GWAS options (PostGSF90)===== =====GWAS options (PostGSF90)=====
 <​file>​OPTION Manhattan_plot</​file>​ <​file>​OPTION Manhattan_plot</​file>​
-Plot using GNUPLOT the Manhattan plot (SNP effects) for each trait and correlated effect.+Uses GNUPLOT ​to plot the Manhattan plot (SNP effects) for each trait and correlated effect.
  
 <​file>​OPTION Manhattan_plot_R</​file>​ <​file>​OPTION Manhattan_plot_R</​file>​
-Plot using R the Manhattan plot (SNP effects) for each trait and correlated effect.\\+Uses to plot the Manhattan plot (SNP effects) for each trait and correlated effect.\\
 ''​pdf''​ images are created: //​manplot_St1e2.pdf//,​ but other formats can be specified.\\ ''​pdf''​ images are created: //​manplot_St1e2.pdf//,​ but other formats can be specified.\\
 Note: //t1e2// corresponds to trait 1, effect 2.\\  Note: //t1e2// corresponds to trait 1, effect 2.\\ 
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 Calculates the variance explained by //n// Mb window of adjacents SNPs.\\ Calculates the variance explained by //n// Mb window of adjacents SNPs.\\
  
 +<​file>​OPTION windows_variance_type n</​file>​
 +Sets windows type for variances calculations:​\\
 +  * 1: moving windows ​
 +  * 2: exclusive windows\\
  
 <​file>​OPTION which_weight x</​file>​ <​file>​OPTION which_weight x</​file>​
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   * 1:  w = y^2 * (2(p(1-p)))   * 1:  w = y^2 * (2(p(1-p)))
   * 2:  w = y^2    * 2:  w = y^2 
-  * 3:  experimental with the degree of brief+  * 3:  experimental with the degree of belief
   * 4:  w = C**(abs(y)/​sqrt(var(y'​s))-2) from VanRaden et al. (2009)   * 4:  w = C**(abs(y)/​sqrt(var(y'​s))-2) from VanRaden et al. (2009)
   * nonlinearA: same as 4   * nonlinearA: same as 4
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 OPTION snp_p_value OPTION snp_p_value
 </​file>​ </​file>​
-Computes p-values for GWAS from elements of the inverse of the Mixed Model Equations previously obtained from blupf90. This requires quite a lot of memory and time. For details see  https://​doi.org/​10.1186/​s12711-019-0469-3.+Computes p-values for GWAS from elements of the inverse of the Mixed Model Equations previously obtained from blupf90. This requires quite a lot of memory and time. For details see  ​[[https://​doi.org/​10.1186/​s12711-019-0469-3|Aguilar et al. (2019)]]. 
 + 
 +<​file>​ 
 +OPTION snp_var 
 +</​file>​ 
 +Creates a file with prediction error covariance (PEC) for SNP to be used in [[http://​nce.ads.uga.edu/​wiki/​doku.php?​id=readme.predf90|PREDF90]] to compute reliability for indirect predictions. This option works when ''​OPTION snp_p_value''​ is used in BLUPF90+.
 =====Output files for GWAS (postGSf90)===== =====Output files for GWAS (postGSf90)=====
  
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   * 1: trait    * 1: trait 
   * 2: effect   * 2: effect
-  * 3: values of SNP effects to use in Manhattan plots+  * 3: values of SNP effects to use in Manhattan plots  -> [abs(SNP_i)/​SD(SNP)]
   * 4: SNP   * 4: SNP
   * 5: Chromosome   * 5: Chromosome
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 <​file>​chrsnp_pval</​file>​ <​file>​chrsnp_pval</​file>​
-contains ​solutions of SNP and weights+contains ​data to create plot by GNUPLOT
  
   * 1: trait    * 1: trait 
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 <​file>​windows_segment</​file>​ <​file>​windows_segment</​file>​
-contains information of windows segments used to get variance ​explainded+contains information of windows segments used to get variance ​explained
   * 1: label   * 1: label
   * 2: window size (number of SNP)   * 2: window size (number of SNP)
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     '​S'​ for solutions of SNP      '​S'​ for solutions of SNP 
     '​V'​ for variance explained     '​V'​ for variance explained
 +    '​P'​ for p-values
     ​     ​
   t1e2   t1e2
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 <​file>​OPTION saveAscii</​file> ​ <​file>​OPTION saveAscii</​file> ​
-Save files intermediate matrices (GimA22i,​G,​Gi,​etc) files as ASCII (default=binary)+Saves files intermediate matrices (GimA22i,​G,​Gi,​etc) files as ASCII (default=binary)
  
  
 <​file>​OPTION saveHinv</​file>​ <​file>​OPTION saveHinv</​file>​
-Save H inverse matrix in Hinv.txt\\+Saves H inverse matrix in Hinv.txt\\
 Format: i,j,val \\ Format: i,j,val \\
 with i,j, the index level for the additive genetic effect with i,j, the index level for the additive genetic effect
  
 <​file>​OPTION saveAinv</​file>​ <​file>​OPTION saveAinv</​file>​
-Save A inverse matrix in Ainv.txt\\+Saves A inverse matrix in Ainv.txt\\
 Format: i,j,val \\ Format: i,j,val \\
 with i,j, the index level for the additive genetic effect with i,j, the index level for the additive genetic effect
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 <​file>​OPTION saveHinvOrig</​file>​ <​file>​OPTION saveHinvOrig</​file>​
-Save the H inverse matrix with original IDs+Saves the H inverse matrix with original IDs
  
        
 <​file>​OPTION saveAinvOrig</​file>​ <​file>​OPTION saveAinvOrig</​file>​
-Save the A inverse matrix with original IDs+Saves the A inverse matrix with original IDs
  
 <​file>​OPTION saveDiagGOrig</​file>​ <​file>​OPTION saveDiagGOrig</​file>​
-Save diagonal of G matrix in DiagGOrig.txt\\+Saves diagonal of G matrix in DiagGOrig.txt\\
 Format: id, val\\ Format: id, val\\
 with id the original IDs  with id the original IDs 
        
 <​file>​OPTION saveGOrig</​file>​ <​file>​OPTION saveGOrig</​file>​
-Save G matrix in G_Orig.txt\\+Saves G matrix in G_Orig.txt\\
 Format: id_i, id_j, val\\ Format: id_i, id_j, val\\
 with id_i and id_j the original IDs with id_i and id_j the original IDs
  
 <​file>​OPTION saveA22Orig</​file>​ <​file>​OPTION saveA22Orig</​file>​
-Save A22 matrix in A22_Orig.txt\\+Saves A22 matrix in A22_Orig.txt\\
 Format: id_i, id_j, val\\ Format: id_i, id_j, val\\
 with id_i and id_j the original IDs with id_i and id_j the original IDs
  
 <​file>​OPTION saveGimA22iOrig </​file>​ <​file>​OPTION saveGimA22iOrig </​file>​
-Save GimA22i matrix in GimA22i_Orig.txt\\+Saves GimA22i matrix in GimA22i_Orig.txt\\
 Format: id_i, id_j, val\\ Format: id_i, id_j, val\\
 with id_i and id_j the original IDs as stored in the renum file with id_i and id_j the original IDs as stored in the renum file
    
 <​file>​OPTION readOrigId</​file>​ <​file>​OPTION readOrigId</​file>​
-Read information from renaddxx.ped file, Original ID and possibly year of birth for its use in parent-progeny conflict output.\\ +Reads information from renaddxx.ped file, Original IDand possibly year of birth for its use in parent-progeny conflict output.\\ 
-Only need if not of the previous ''​save*Orig'' ​are present. ​  +Only need if none of the previous ''​save*Orig'' ​is present. ​  
  
 <​file>​OPTION saveGimA22iRen </​file>​ <​file>​OPTION saveGimA22iRen </​file>​
-Save GimA22i matrix in GimA22i_Ren.txt\\+Saves GimA22i matrix in GimA22i_Ren.txt\\
 Format: id_i, id_j, val\\ Format: id_i, id_j, val\\
 with id_i and id_j the IDs as read from the data/​pedigree file with id_i and id_j the IDs as read from the data/​pedigree file
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 <​file>​OPTION savePLINK</​file>​ <​file>​OPTION savePLINK</​file>​
-Save Genotype in ''​PLINK''​ format \\+Saves Genotype in ''​PLINK''​ format \\
 files: toPLINK.ped and toPLINK.map ​ files: toPLINK.ped and toPLINK.map ​
  
 <​file>​OPTION no_full_binary</​file>​ <​file>​OPTION no_full_binary</​file>​
-Save the elements of half-matrix instead of the full matrix. It is useful to keep the compatibility with the older version of preGSf90.\\+Saves the elements of half-matrix instead of the full matrix. It is useful to keep the compatibility with the older version of preGSf90. The newer versions save the matrix in a more efficient way, where reading the information from the binary file is not trivial (i.e., not as i, j, val anymore).\\
  
 =====Save and Read intermediate files===== =====Save and Read intermediate files=====
  
 <​file>​OPTION readGimA22i file </​file>​ <​file>​OPTION readGimA22i file </​file>​
-This option is used in analyses ​programs (BLUPF90,​REMLF90,​ etc.) in order to use matrices ​stored in ''​GimA22i''​ file (default filename).\\ +This option is used in the application ​programs (BLUPF90,​REMLF90,​ etc.) to use the information already ​stored in ''​GimA22i''​ file (default filename).\\ 
-In general methods used to create and invert matrices in such programs ​dont use optimized version.\\ +In generalmethods used to create and invert matrices in such programs ​don'​t ​use an optimized version.\\ 
-For large number of genotyped animals run first ''​PreGSf90''​ and the read stored matrices in analyses programs.\\+For large number of genotyped animals run first ''​PreGSf90''​ and the read stored matrices in analyses programs.\\
  
-Optional //file// can be used to specify ​other filename or path, for example ''​OPTION readGimA22i ../​../​pregsrun/​GimA22i''​.\\+Optional //file// can be used to specify ​a different ​filename ​(other than ''​GimA22i''​) ​or path, for example ''​OPTION readGimA22i ../​../​pregsrun/​GimA22i''​.\\
  
  
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 =====DEPRECATED OPTIONS===== =====DEPRECATED OPTIONS=====
 <​file>​OPTION chrinfo file </​file>​ \\ <​file>​OPTION chrinfo file </​file>​ \\
 +
 +This is deprecated. Use instead ''​OPTION map_file''​.
 +
 Read SNP map information from //file//.\\ Read SNP map information from //file//.\\
  
readme.pregsf90.1590165716.txt.gz · Last modified: 2020/05/22 16:41 by dani