Differences

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--- ped [2011/06/07 16:40] – heidi
+++ ped [2011/06/08 09:42] (current) – heidi
@@ Line 6: / Line 6: @@
 \\
 PED\\
-NewHybrids is a program for computing the posterior distribution that individuals in a sample fall into different hybrid categories.
+The "ped" file format refers to the widely-used format for linkage pedigree data and used as input for the program PLINK. PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
 \\
 ===== Program information =====
+  * written in C/C++
   * Mac
   * Windows
+  * Unix
 \\
@@ Line 23: / Line 27: @@
 ===== Data type handled =====
   * diploid
-  * AFLP
+  * SNP
-  * MICROSAT
-  * Standard
 \\
@@ Line 37: / Line 42: @@
 ===== Input Files =====
-  * whitespace (spaces and or tabs) separated text file *.txt/*.dat
+  * whitespace (spaces and or tabs) separated text file *.ped
-  * first line: ''NumIndivs '' number of individuals
+  * each line correspond to one individual
-  * second line: ''NumLoci '' number of loci
+  * following first 6 columns are mandatory (The IDs are alphanumberic):
-  * third line: ''Digits '' number of digits used to denote a particular allele
+    * ''Family ID''
-  * fourth line: ''Format '' ''Lumped'' (genotype at a single locus is given by a single number) or ''NonLumped''
+    * ''Individual ID''
-  * next lines: ''LocusNames'' names of all loci separated by whitespace
+    * ''Paternal ID''
-  * next lines: genotype data
+    * ''Maternal ID''
-    * first character: number of the individual (numbering must be serially)
+    * ''Sex'' (1=male; 2=female; any other character=unknown)
-    * next characters: genotypes (all on same line or on different lines)
+    * ''Phenotype'' (only 1 phenotype! The phenotype can be either a quantitative trait or an affection status column: PLINK will automatically detect which type (i.e. based on whether a value other than 0, 1, 2 or the missing genotype code is observed))
-      * ''Lumped'' format: two alleles are encoded as one number, ''Digits'' specify how many digits are used to represent each locus
+  * Comments: line starts with ''#''
-      * ''NonLumped'' format: alleles at each locus are given by a consecutive pair of numbers that are white space seperated
+  * Affection status, by default, should be coded:
-      * Missing data: ''Lumped'': encoded as ''0'', ''NonLumped'': encoded as ''-1'' (each allele at the missing locus must have a ''-1'')
+    * -9 missing
+    * 0 missing
+    * 1 unaffected
+    * 2 affected
+  * column 7 onwards: Genotypes
+    * any character (e.g.: 1,2,3,4 or A,C,G,T or anything else)
+    * missing genotype: ''0''
+    * all markers must be biallelic (diploid). Either both alleles should be missing or neither. Haploid data: encode them as diploid homozygot. Two alleles are shown after each other.
 \\
+If specially specified following columns can be missing:
+  * ''Family ID''
+  * ''Individual ID''
+  * ''Paternal ID'' and ''Maternal ID''
+  * ''Sex''
+  * ''Phenotype''
+\\
-==== AFLP data ====
-  * ''Lumped'' format
-  * ''+'' band is present
-  * ''-'' band is absent
-  * ''0'' missing data
-  * data types can be mixed
+==== MAP files ====
+  * Each line of the MAP file describes a single marker and must contain exactly 4 columns:
+    * 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 ====
-  * ''Lumped'' data file:
+  * PED files:
 <code>
-NumIndivs 2
+FAM001  1  0 0  1  2  A A  G G  A C
-NumLoci 6
+FAM001  2  0 0  1  2  A A  A G  0 0
-Digits 1
-Format Lumped
-LocusNames sAAT1 sAAT2 sAAT3 ADA1 ADA2 ADH
-11 11 11 0 11 32
- 21 11 21 11 11 12
 </code>
-  * ''NonLumped'' data file:
 <code>
-NumIndivs 2
+ 1 0 0 1   1   A A    A A    A A    A A    A A
-NumLoci 6
+ 1 0 0 1   1   A C    A C    A C    A C    A C
-Digits 1
+1 0 0 2   1   A A    A A    A A    A A    A A
-Format NonLumped
+1 0 0 2   1   A C    A C    A C    A C    A C
-LocusNames sAAT1 sAAT2 sAAT3 ADA1 ADA2 ADH
- 123 143 -1 -1 144 144 120 122 157 158 144 144
- 135 135 134 140 144 144 120 122 161 161 144 144
 </code>
-  * AFLP data file (4 Microsat loci, 5 AFLP loci):
+  * MAP files:
 <code>
-NumIndivs 2
+  rs123456  0  1234555
-NumLoci 9
+  rs234567  0  1237793
-Digits 1
+  rs224534  0  -1237697
-Format Lumped
+  rs233556  0  1337456
-LocusNames m1 m2 m3 m4 A1 A2 A3 A4 A5
- 11 12 13 11 + + + - +
-22 33 11 22 - - 0 - -
-12 13 13 11 + - - - +
 </code>
+<code>
+    snp1   0   1000
+X    snp2   0   1000
+Y    snp3   0   1000
+XY   snp4   0   1000
+MT   snp5   0   1000
+</code>
+\\
 ===== How to cite =====
-Anderson, E.C. and Thompson, E.A. (2002) A model-based method for identifying species hybrids using multilocus genetic data. Genetics 160: 1217-1229.
+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 linkage analysis. American Journal of Human Genetics, 81.