Detritus Wiki

Ejemplo de mezclar dos DB:

$ plink --bfile AD/AD_QC --bmerge Controles/Cont_QC.bed Controles/Cont_QC.bim Controles/Cont_QC.fam --make-bed --out Merged/ADMur

Esto mezcla las DBs AD_QC y Cont_QC para hacer una sola en Merged,

@----------------------------------------------------------@
|        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 [ Merged/ADMur.log ]
Analysis started: Tue Mar 12 09:10:57 2013

Options in effect:
	--bfile AD/AD_QC
	--bmerge Controles/Cont_QC.bed Controles/Cont_QC.bim Controles/Cont_QC.fam
	--make-bed
	--out Merged/ADMur

Reading map (extended format) from [ AD/AD_QC.bim ] 
212561 markers to be included from [ AD/AD_QC.bim ]
Reading pedigree information from [ AD/AD_QC.fam ] 
329 individuals read from [ AD/AD_QC.fam ] 
329 individuals with nonmissing phenotypes
Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
Missing phenotype value is also -9
329 cases, 0 controls and 0 missing
94 males, 235 females, and 0 of unspecified sex
Reading genotype bitfile from [ AD/AD_QC.bed ] 
Detected that binary PED file is v1.00 SNP-major mode
Using merge mode 1 : consensus call (default)

216526 markers to be merged from [ Controles/Cont_QC.bim ]
Of these, 11842 are new, 204684 already exist in current data
801 individuals merged from [ Controles/Cont_QC.fam ] 
Of these, 801 were new, 0 were already in current data

Detected that binary PED file is v1.00 SNP-major mode
1130 individuals with nonmissing phenotypes
Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
Missing phenotype value is also -9
329 cases and 801 controls
Before frequency and genotyping pruning, there are 224403 SNPs
1130 founders and 0 non-founders found
1200 heterozygous haploid genotypes; set to missing
Writing list of heterozygous haploid genotypes to [ Merged/ADMur.hh ]
Total genotyping rate in remaining individuals is 0.953049
0 SNPs failed missingness test ( GENO > 1 )
0 SNPs failed frequency test ( MAF < 0 )
After frequency and genotyping pruning, there are 224403 SNPs
After filtering, 329 cases, 801 controls and 0 missing
After filtering, 527 males, 603 females, and 0 of unspecified sex
Writing pedigree information to [ Merged/ADMur.fam ] 
Writing map (extended format) information to [ Merged/ADMur.bim ] 
Writing genotype bitfile to [ Merged/ADMur.bed ] 
Using (default) SNP-major mode

Analysis finished: Tue Mar 12 09:11:52 2013

$ ls Merged/
ADMur.bed  ADMur.bim  ADMur.fam  ADMur.hh  ADMur.log

$ wc -l Merged/*
  172101 Merged/ADMur.bed
  224403 Merged/ADMur.bim
    1130 Merged/ADMur.fam
    1200 Merged/ADMur.hh
      62 Merged/ADMur.log
  398896 total

Ahora la trato de convertir en ped y map

$ plink --bfile Merged/ADMur --recode --out Converted/ADMur

@----------------------------------------------------------@
|        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 [ Converted/ADMur.log ]
Analysis started: Tue Mar 12 09:16:59 2013

Options in effect:
	--bfile Merged/ADMur
	--recode
	--out Converted/ADMur

Reading map (extended format) from [ Merged/ADMur.bim ] 
224403 markers to be included from [ Merged/ADMur.bim ]
Reading pedigree information from [ Merged/ADMur.fam ] 
1130 individuals read from [ Merged/ADMur.fam ] 
1130 individuals with nonmissing phenotypes
Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
Missing phenotype value is also -9
329 cases, 801 controls and 0 missing
527 males, 603 females, and 0 of unspecified sex
Reading genotype bitfile from [ Merged/ADMur.bed ] 
Detected that binary PED file is v1.00 SNP-major mode
Before frequency and genotyping pruning, there are 224403 SNPs
1130 founders and 0 non-founders found
1200 heterozygous haploid genotypes; set to missing
Writing list of heterozygous haploid genotypes to [ Converted/ADMur.hh ]
Total genotyping rate in remaining individuals is 0.953049
0 SNPs failed missingness test ( GENO > 1 )
0 SNPs failed frequency test ( MAF < 0 )
After frequency and genotyping pruning, there are 224403 SNPs
After filtering, 329 cases, 801 controls and 0 missing
After filtering, 527 males, 603 females, and 0 of unspecified sex
Writing recoded ped file to [ Converted/ADMur.ped ] 
Writing new map file to [ Converted/ADMur.map ] 

Analysis finished: Tue Mar 12 09:18:27 2013

$ wc -l Converted/*
      1200 Converted/ADMur.hh
        47 Converted/ADMur.log
    224403 Converted/ADMur.map
      1130 Converted/ADMur.ped
    226780 total

Ya esta preparado para convertirlo a formato de impute