read.trio: format the parental genotype in vcf file

In yanjunzan/GBSA: Genotype imputation and QTL mapping with ultra low coverage sequencing in pedigree

Description

Give two parental ID in a divergent cross, this function screen the called sites

Usage

read_trio(of_id,F_id,M_id,vcf.file,pathout,generate.input)

Arguments

of_id	offspring ID in the vcf file
F_id	one of the parental ID in the vcf file,does not have to be father line id
M_id	one of the parental ID in the vcf file,does not have to be mother line id
vcf.file	the input vcf, this file should be filtered in advance to make sure only fixed sites between lines are included
pathout	out put path
generate.input	T means only generate intermediate files, F means read in the intermediate file

Details

We recommend a two step run: i) turn on generate.input to create the intermediate file only; ii) turn off the generate.input to read in the data.

Value

return a data.table object with gentoype of the divergent lines and this indiviudal in columns. Each row is a site which is fixed between parental and has genotype call for this particular offspring.

Author(s)

Yanjun Zan, Thibaut Payen

References

Yanjun Zan, Thibaut Payen, Leif Andersson, Paul B. Siegel and <c3><96>rjan Carlborg;Whole-genome QTL mapping in experimental pedigrees from outbred founders utilizing low coverage individual based sequencing 2018

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

yanjunzan/GBSA documentation built on May 14, 2019, 4:05 a.m.