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genetica:pre_1kg [2013/05/06 14:38]
osotolongo [Eligiendo solo los europeos]
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>
Line 190: Line 192:
 $ grep -f individuals.txt ../ALL/all_chr1.fam > eur_pop.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 --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.1367851134.txt.gz · Last modified: 2020/08/04 10:48 (external edit)