format_fixed: format the genotype in the vcf file

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

Description

Give four grand parental ID in a divergent cross, this function screen the fixed sites between divergent parental lines and extract those called sites in an offspring.

Usage

format_fixed(pedigreeTable, vcf.file, pathout,Core=5,pattern=paste("(^F2_",of_id,".*)|(^",of_id,"_F2.*)",sep=""))

Arguments

pedigreeTable	a data.frame with 7 columns with names as id.f2, id.f2.ma, id.f2.fa, fa.h, ma.h, ma.l, fa.l. Those are F2 id, corresponding mother id,father id and grand parent ids, fa.h,ma.h must come from one line and ma.l, fa.l. from another divergent line
vcf.file	the input vcf, this file should be filtered in advance to make sure only fixed sites between lines are included
pathout	output path
pattern	the pattern used for mathing individual names in vcf files, eg. we have a individual named as 350 in pedigree file, but named as F2_350_S73_L001.variant462.variant2.variant in vcf file

Value

this would write out a few intermediate files

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

See the package tutorial

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