rossibarra / phasing_tests

#Phasing Code

Uses selfed progeny from a single mom to

1. impute mom's genotype
2. phase mom
3. impute self progeny genotypes

Currently assumes data is coded as 0: AA 1: Aa 2: aa and 3 for missing data.

---

split JRI's codes and test independently

### loading all the functions in folder "lib"
sourceall <-function(rm=FALSE){
    if(rm) rm(list=ls())
    f <- sapply(list.files(pattern="[.]R$", path="lib", full.names=TRUE), source)
}
sourceall(rm=T)

---

File Formats (PLINK format)

It accepts sequences of the form 0/1/2/3 where 0/2 denote the genotypes that are homozygous, 1 denotes a heterozygous genotype, and 3 denotes an unknown genotype.

The PED file format is as follows (plink --no-sex, --no-pheno):

• tab delimited
• 'family ID' 'plant ID' 'Paternal ID' 'Maternal ID' 'genotype sequence'

The MAP file format

• 'chr' 'SNPID' 'Base-pair position' 'genetic position'

For example: