Differences

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--- genetica:pre_1kg [2013/05/06 09:56] – [Preprocesando con plink] osotolongo
+++ genetica:pre_1kg [2020/08/04 10:58] (current) – external edit 127.0.0.1
@@ Line 162: / Line 162: @@
 Primero hay que recodificar los alelos a ACGT y de paso los pasamos a binario (solo es necesario si hemos converitdo con el primer metodo)
-** Cuidado: ** Hay que garantizar que el orden de los archivos sea el correcto para que el archivo resultante empiece por el cromosoma 1
+** Cuidado: ** Hay que garantizar que el orden de los archivos sea el correcto para que el archivo resultante empiece por el cromosoma 1 (opcion //-v// de //ls//)
 <code bash>
@@ Line 174: / Line 174: @@
 <code bash>
-afr=(`ls *.bed`);
+afr=(`ls -v all_chr*.bed`);
 for (( i=1; i<${#afr[@]}; i++ ));
 do
@@ Line 181: / Line 181: @@
 done;
 x=${afr[0]};
-plink --bfile ${x%.bed} --merge-list allfiles.txt --make-bed --out 1000genome_CEU_merged
+plink --bfile ${x%.bed} --merge-list allfiles.txt --make-bed --out 1000genome_all_merged
 </code>
+===== Eligiendo solo los europeos ======
+Lo que quiero es seleccionar la [[http://www.1000genomes.org/category/frequently-asked-questions/samples|poblacion europea]] de todo el estudio.
+<code>
+$ awk {'if ($3=="EUR") print $1'} /media/1000Genome/phase1_integrated_calls.20101123.ALL.panel > individuals.txt
+$ grep -f individuals.txt ../ALL/all_chr1.fam > eur_pop.txt
+$ plink --bfile ../ALL/1000genome_all_merged --keep eur_pop.txt --make-bed --out 1000genome_eur
+@----------------------------------------------------------@
+|        PLINK!       |     v1.07      |   10/Aug/2009     |
+|----------------------------------------------------------|
+|  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
+|----------------------------------------------------------|
+|  For documentation, citation & bug-report instructions:  |
+|        http://pngu.mgh.harvard.edu/purcell/plink/        |
+@----------------------------------------------------------@
+Web-based version check ( --noweb to skip )
+Connecting to web...  OK, v1.07 is current
+Writing this text to log file [ 1000genome_eur.log ]
+Analysis started: Mon May  6 16:38:21 2013
+Options in effect:
+        --bfile ../ALL/1000genome_all_merged
+        --keep eur_pop.txt
+        --make-bed
+        --out 1000genome_eur
+Reading map (extended format) from [ ../ALL/1000genome_all_merged.bim ]
+39706712 markers to be included from [ ../ALL/1000genome_all_merged.bim ]
+Reading pedigree information from [ ../ALL/1000genome_all_merged.fam ]
+individuals read from [ ../ALL/1000genome_all_merged.fam ]
+individuals with nonmissing phenotypes
+Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
+Missing phenotype value is also -9
+cases, 0 controls and 1092 missing
+males, 0 females, and 1092 of unspecified sex
+Warning, found 1092 individuals with ambiguous sex codes
+Writing list of these individuals to [ 1000genome_eur.nosex ]
+Reading genotype bitfile from [ ../ALL/1000genome_all_merged.bed ]
+Detected that binary PED file is v1.00 SNP-major mode
+Reading individuals to keep [ eur_pop.txt ] ... 379 read
+individuals removed with --keep option
+Before frequency and genotyping pruning, there are 39706712 SNPs
+founders and 0 non-founders found
+Total genotyping rate in remaining individuals is 1
+SNPs failed missingness test ( GENO > 1 )
+SNPs failed frequency test ( MAF < 0 )
+After frequency and genotyping pruning, there are 39706712 SNPs
+After filtering, 0 cases, 0 controls and 379 missing
+After filtering, 0 males, 0 females, and 379 of unspecified sex
+Writing pedigree information to [ 1000genome_eur.fam ]
+Writing map (extended format) information to [ 1000genome_eur.bim ]
+Writing genotype bitfile to [ 1000genome_eur.bed ]
+Using (default) SNP-major mode
+Analysis finished: Mon May  6 16:59:16 2013
+</code>
 ===== y ya ta =====
 Ahora hay que seguir fundiendo la DB que tenemos con nuestros datos: [[plink_1kg_impute| para poder imputar]]
-===== porqueria que puede pasar ======
+====== porqueria que puede pasar =======
 ==== DUPLICATE MARKERS FOUND ====
@@ Line 296: / Line 357: @@
 <code>
-$ plink --bfile all_chr10 --merge-list allfiles.txt --make-bed --out 1000genome_all_merged --exclude rmsnps.txt --allow-no-sex
+$ plink --bfile all_chr1 --merge-list /home/osotolongo/data/test_impute/mkgendb/allfiles.txt --make-bed --out 1000genome_all_merged --exclude /home/osotolongo/data/test_impute/mkgendb/rmsnps.txt --allow-no-sex
-@----------------------------------------------------------@
-|        PLINK!       |     v1.07      |   10/Aug/2009     |
-|----------------------------------------------------------|
-|  (C) 2009 Shaun Purcell, GNU General Public License, v2  |
-|----------------------------------------------------------|
-|  For documentation, citation & bug-report instructions:  |
-|        http://pngu.mgh.harvard.edu/purcell/plink/        |
-@----------------------------------------------------------@
-Web-based version check ( --noweb to skip )
-Recent cached web-check found... OK, v1.07 is current
-Writing this text to log file [ 1000genome_all_merged.log ]
-Analysis started: Fri May  3 12:56:36 2013
-Options in effect:
-	--bfile all_chr10
-	--merge-list allfiles.txt
-	--make-bed
-	--out 1000genome_all_merged
-	--exclude rmsnps.txt
-	--allow-no-sex
-Reading map (extended format) from [ all_chr10.bim ]
-1882663 markers to be included from [ all_chr10.bim ]
-Reading pedigree information from [ all_chr10.fam ]
-individuals read from [ all_chr10.fam ]
-individuals with nonmissing phenotypes
-Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
-Missing phenotype value is also -9
-cases, 0 controls and 1092 missing
-males, 0 females, and 1092 of unspecified sex
-Warning, found 1092 individuals with ambiguous sex codes
-Writing list of these individuals to [ 1000genome_all_merged.nosex ]
-Reading genotype bitfile from [ all_chr10.bed ]
-Detected that binary PED file is v1.00 SNP-major mode
-Using merge mode 1 : consensus call (default)
-Detected that binary PED file is v1.00 SNP-major mode
-Detected that binary PED file is v1.00 SNP-major mode
-Detected that binary PED file is v1.00 SNP-major mode
-Detected that binary PED file is v1.00 SNP-major mode
-Detected that binary PED file is v1.00 SNP-major mode
-Detected that binary PED file is v1.00 SNP-major mode
-Detected that binary PED file is v1.00 SNP-major mode
-Detected that binary PED file is v1.00 SNP-major mode
-Detected that binary PED file is v1.00 SNP-major mode
-Detected that binary PED file is v1.00 SNP-major mode
-Detected that binary PED file is v1.00 SNP-major mode
-Detected that binary PED file is v1.00 SNP-major mode
-Detected that binary PED file is v1.00 SNP-major mode
-Detected that binary PED file is v1.00 SNP-major mode
-Detected that binary PED file is v1.00 SNP-major mode
-Detected that binary PED file is v1.00 SNP-major mode
-Detected that binary PED file is v1.00 SNP-major mode
-Detected that binary PED file is v1.00 SNP-major mode
-Detected that binary PED file is v1.00 SNP-major mode
-Detected that binary PED file is v1.00 SNP-major mode
-Detected that binary PED file is v1.00 SNP-major mode
-Detected that binary PED file is v1.00 SNP-major mode
-Merging 22 samples, final sample contains 1092 individuals and 39706715 markers
-Reading list of SNPs to exclude [ rmsnps.txt ] ... 3 read
-Before frequency and genotyping pruning, there are 39706712 SNPs
-founders and 0 non-founders found
-Total genotyping rate in remaining individuals is 1
-SNPs failed missingness test ( GENO > 1 )
-SNPs failed frequency test ( MAF < 0 )
-After frequency and genotyping pruning, there are 39706712 SNPs
-After filtering, 0 cases, 0 controls and 1092 missing
-After filtering, 0 males, 0 females, and 1092 of unspecified sex
-Writing pedigree information to [ 1000genome_all_merged.fam ]
-Writing map (extended format) information to [ 1000genome_all_merged.bim ]
-Writing genotype bitfile to [ 1000genome_all_merged.bed ]
-Using (default) SNP-major mode
-Analysis finished: Fri May  3 17:11:00 2013
 </code>