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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 R 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 ID, and 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 general, methods 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 a 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 a 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//.\\ | ||