Differences

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--- genetica:pre_1kg [2013/05/06 14:38] – [Eligiendo solo los europeos] osotolongo
+++ genetica:pre_1kg [2020/08/04 10:58] (current) – external edit 127.0.0.1
@@ 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>
@@ Line 190: / Line 192: @@
 $ 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 =====
@@ Line 303: / Line 357: @@
 <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>