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genetica:pre_1kg [2013/05/06 12:33]
osotolongo [porqueria que puede pasar]
genetica:pre_1kg [2020/08/04 10:58] (current)
Line 181: Line 181:
 done; done;
 x=${afr[0]}; x=${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> </code>
  
 ===== Eligiendo solo los europeos ====== ===== 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> <code>
 $ awk {'if ($3=="EUR") print $1'} /media/1000Genome/phase1_integrated_calls.20101123.ALL.panel > individuals.txt $ 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 $ grep -f individuals.txt ../ALL/all_chr1.fam > eur_pop.txt
-$ plink --bfile ../1000genome_all_merged --keep eur_pop.txt --make-bed --out 1000genome_eur+$ 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 ] 
 +1092 individuals read from [ ../ALL/1000genome_all_merged.fam ] 
 +0 individuals with nonmissing phenotypes 
 +Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) 
 +Missing phenotype value is also -9 
 +0 cases, 0 controls and 1092 missing 
 +0 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 
 +713 individuals removed with --keep option 
 +Before frequency and genotyping pruning, there are 39706712 SNPs 
 +379 founders and 0 non-founders found 
 +Total genotyping rate in remaining individuals is 1 
 +0 SNPs failed missingness test ( GENO > 1 ) 
 +0 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> </code>
 ===== y ya ta ===== ===== y ya ta =====
Line 303: Line 357:
  
 <code> <code>
- +$ 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
 </code> </code>
genetica/pre_1kg.1367843638.txt.gz · Last modified: 2020/08/04 10:48 (external edit)