convert_gbs2plink: 'Change gbs hmp to plink format'

In yangjl/huskeR: Genomic and Genetic analysis Pipeline on HPC

Description

load gbs file, change to tfile format for PLINK, filtering multiple alleles and then change to "A A" coding and change IUPAC Ambiguity Codes

Usage

convert_gbs2plink(gbsfile = "g2f_2014_zeagbsv27v5hmp_nodash.txt",
  gbs = NULL, iupac = TRUE, mode = 1,
  outfile = "~/dbcenter/seeds_data/chr10_filetered_unimputed.bed")

run_iupac(subg)

Arguments

gbsfile	An input gbs in hmp format. Note without # lines. [chr, ="g2f_2014_zeagbsv27v5hmp_nodash.txt"]
gbs	If gbsfile is NULL load this gbs object. [obj, data.table=NULL]
iupac	Change the IUPAC Code. [logical, =TRUE]
mode	GBS code mode. mode=1, A, T, C, G; mode=2, AA, TT, CC, GG. [num, =1]
outfile	Output file name. [chr, ="~/dbcenter/seeds_data/chr10_filetered_unimputed.bed"]
jmph	plink –tped test.tped –tfam test.tfam –make-bed –missing-genotype N –allow-no-sex –make-founders –out ../Data/sim

yangjl/huskeR documentation built on Sept. 2, 2021, 5:38 a.m.