ped
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====== PED ====== | ====== PED ====== | ||
\\ | \\ | ||
- | **[[http://ib.berkeley.edu/labs/slatkin/eriq/ | + | **[[http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#ped|PED]]**\\ |
- | [[http:// | + | |
\\ | \\ | ||
- | PED version 1.1 beta (7. April 2003)\\ | + | PED\\ |
- | NewHybrids is a program | + | The " |
\\ | \\ | ||
+ | |||
===== Program information ===== | ===== Program information ===== | ||
+ | * written in C/C++ | ||
* Mac | * Mac | ||
* Windows | * Windows | ||
+ | * Unix | ||
\\ | \\ | ||
+ | |||
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===== Data type handled ===== | ===== Data type handled ===== | ||
* diploid | * diploid | ||
- | * AFLP | + | * SNP |
- | * MICROSAT | + | |
- | * Standard | + | |
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+ | |||
+ | |||
+ | |||
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===== Input Files ===== | ===== Input Files ===== | ||
- | * whitespace (spaces and or tabs) separated text file *.txt/*.dat | + | * whitespace (spaces and or tabs) separated text file *.ped |
- | * first line: '' | + | |
- | * second line: '' | + | * following |
- | * third line: '' | + | * '' |
- | * fourth line: '' | + | * '' |
- | * next lines: '' | + | * '' |
- | * next lines: genotype data | + | * '' |
- | * first character: number of the individual (numbering must be serially) | + | * '' |
- | * next characters: genotypes | + | * '' |
- | * '' | + | * Comments: line starts with '' |
- | * '' | + | * Affection status, by default, should be coded: |
- | * Missing | + | * -9 missing |
+ | * 0 missing | ||
+ | * 1 unaffected | ||
+ | * 2 affected | ||
+ | * column 7 onwards: Genotypes | ||
+ | * any character | ||
+ | * missing genotype: '' | ||
+ | * all markers must be biallelic (diploid). Either both alleles | ||
\\ | \\ | ||
+ | If specially specified following columns can be missing: | ||
+ | * '' | ||
+ | * '' | ||
+ | * '' | ||
+ | * '' | ||
+ | * '' | ||
+ | |||
+ | \\ | ||
+ | |||
- | ==== AFLP data ==== | ||
- | * '' | ||
- | * '' | ||
- | * '' | ||
- | * '' | ||
- | | + | ==== MAP files ==== |
+ | | ||
+ | * chromosome (1-22, X, Y, MT or 0 if unplaced) | ||
+ | * rs# or snp identifier | ||
+ | * Genetic distance (morgans) (missing: 0) | ||
+ | * Base-pair position (bp units) (Base-pair positions are expected to correspond to positive integers within the range of typical human chromosome sizes) | ||
+ | * The MAP file must contain as many markers as are in the PED file. | ||
+ | * The markers in the PED file do not need to be in genomic order: (i.e. the order MAP file should align with the order of the PED file markers). | ||
\\ | \\ | ||
+ | |||
+ | |||
+ | |||
==== Example ==== | ==== Example ==== | ||
- | * '' | + | * PED files: |
< | < | ||
- | NumIndivs 2 | + | FAM001 |
- | NumLoci 6 | + | FAM001 |
- | Digits | + | |
- | Format Lumped | + | |
- | LocusNames sAAT1 sAAT2 sAAT3 ADA1 ADA2 ADH | + | |
- | 1 11 11 11 0 11 32 | + | |
- | 2 21 11 21 11 11 12 | + | |
</ | </ | ||
- | * '' | ||
< | < | ||
- | NumIndivs 2 | + | 1 1 0 0 1 |
- | NumLoci 6 | + | 2 1 0 0 1 |
- | Digits | + | 3 1 0 0 2 1 A A A A A A A A A A |
- | Format NonLumped | + | 4 1 0 0 2 |
- | LocusNames sAAT1 sAAT2 sAAT3 ADA1 ADA2 ADH | + | |
- | 1 123 143 -1 -1 144 144 120 122 157 158 144 144 | + | |
- | 2 135 135 134 140 144 144 120 122 161 161 144 144 | + | |
</ | </ | ||
- | * AFLP data file (4 Microsat loci, 5 AFLP loci): | + | * MAP files: |
< | < | ||
- | NumIndivs 2 | + | 1 rs123456 |
- | NumLoci 9 | + | 1 |
- | Digits | + | 1 |
- | Format Lumped | + | 1 rs233556 |
- | LocusNames m1 m2 m3 m4 A1 A2 A3 A4 A5 | + | |
- | 1 11 12 13 11 + + + - + | + | |
- | 2 22 33 11 22 - - 0 - - | + | |
- | 3 12 13 13 11 + - - - + | + | |
</ | </ | ||
+ | |||
+ | < | ||
+ | 1 snp1 | ||
+ | X snp2 | ||
+ | Y snp3 | ||
+ | XY | ||
+ | MT | ||
+ | </ | ||
+ | | ||
+ | \\ | ||
===== How to cite ===== | ===== How to cite ===== | ||
- | Anderson, E.C. and Thompson, E.A. (2002) A model-based | + | Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ & Sham PC (2007) PLINK: a toolset for whole-genome association and population-based |
ped.1307457560.txt.gz · Last modified: 2011/06/07 16:39 by heidi